R3KG65 last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.096290

pubchem
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.096290

Other names: pubchem

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links in the homepage.

Webpage:

http://pubchem.ncbi.nlm.nih.gov/

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Name: PubChem Attribution required
URL: https://pubchemdocs.ncbi.nlm.nih.gov/citation-guidelines

Publications: (9)

Publications
More detailed information about this field from each metasource.

PubChem 2019 update: improved access to chemical data
PMID: 30371825
metasource: Fairsharing.org
version: FAIRsharing.org: PubChem; PubChem; DOI: https://doi.org/10.25504/FAIRsharing.qt3w7z; Last edited: April 26, 2021, 12:02 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

PubChem: a public information system for analyzing bioactivities of small molecules
PMID: 19498078
metasource: Fairsharing.org
version: FAIRsharing.org: PubChem; PubChem; DOI: https://doi.org/10.25504/FAIRsharing.qt3w7z; Last edited: April 26, 2021, 12:02 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Database resources of the National Center for Biotechnology Information
PMID: 17170002
metasource: Fairsharing.org
version: FAIRsharing.org: PubChem; PubChem; DOI: https://doi.org/10.25504/FAIRsharing.qt3w7z; Last edited: April 26, 2021, 12:02 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

PubChem's BioAssay Database
PMID: 22140110
metasource: Fairsharing.org
version: FAIRsharing.org: PubChem; PubChem; DOI: https://doi.org/10.25504/FAIRsharing.qt3w7z; Last edited: April 26, 2021, 12:02 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.096290

PubChem BioAssay: 2017 update
PMID: 27899599
metasource: Fairsharing.org
version: FAIRsharing.org: PubChem; PubChem; DOI: https://doi.org/10.25504/FAIRsharing.qt3w7z; Last edited: April 26, 2021, 12:02 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

An overview of the PubChem BioAssay resource
PMID: 19933261
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.096290

PubChem as a public resource for drug discovery
PMID: 20970519
metasource: Fairsharing.org
version: FAIRsharing.org: PubChem; PubChem; DOI: https://doi.org/10.25504/FAIRsharing.qt3w7z; Last edited: April 26, 2021, 12:02 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

PubChem BioAssay: 2014 update
PMID: 24198245
metasource: Fairsharing.org
version: FAIRsharing.org: PubChem; PubChem; DOI: https://doi.org/10.25504/FAIRsharing.qt3w7z; Last edited: April 26, 2021, 12:02 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

http://dx.doi.org/10.1093/nar/gkaa971
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

PubChem 2019 update: improved access to chemical data PubMed citations: 677.

677 articles citing: PubChem 2019 update: improved access to chemical data

Repurposing Drugs via Network Analysis: Opportunities for Psychiatric Disorders. PMID:35890359
Vietnamese Dalbergia tonkinensis: A Promising Source of Mono- and Bifunctional Vasodilators. PMID:35889386
Expression patterns and therapeutic implications of CDK4 across multiple carcinomas: a molecular docking and MD simulation study. PMID:35870089
Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum. PMID:35865963
Network Pharmacology-Based Prediction and Pharmacological Validation of Effects of Astragali Radix on Acetaminophen-Induced Liver Injury. PMID:35860733
Network Pharmacological Study on the Mechanism of Cynanchum paniculatum (Xuchangqing) in the Treatment of Bungarus multicinctus Bites. PMID:35837378
Andrographolide induces anti-SARS-CoV-2 response through host-directed mechanism: an in silico study. PMID:35812188
The role of eugenol and ferulic acid as the competitive inhibitors of transcriptional regulator RhlR in P. aeruginosa. PMID:35800985
Recent Advances in Cancer Drug Discovery Through the Use of Phenotypic Reporter Systems, Connectivity Mapping, and Pooled CRISPR Screening. PMID:35795568
Significance of the spectral correction of photon counting detector response in material classification from spectral x-ray CT. PMID:35789704
Exploring the Mechanism of Hawthorn Leaves Against Coronary Heart Disease Using Network Pharmacology and Molecular Docking. PMID:35783840
Discovery of Drug Candidates for Specific Human Disease Based on Natural Products of Gut Microbes. PMID:35783383
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer. PMID:35778754
Fully Flexible Ligand Docking for the P2X7 Receptor Using ROSIE. PMID:35776320
Implementation of Chemical Health, Safety, and Environmental Risk Assessment in Laboratories: A Case-Series Study. PMID:35774572
Repositioning of Anti-Inflammatory Drugs for the Treatment of Cervical Cancer Sub-Types. PMID:35770086
A brief review of protein-ligand interaction prediction. PMID:35765652
Network pharmacology integrated molecular dynamics reveals the bioactive compounds and potential targets of Tinospora crispa Linn. as insulin sensitizer. PMID:35737707
Targeting cyclin-dependent kinase 1 (CDK1) in cancer: molecular docking and dynamic simulations of potential CDK1 inhibitors. PMID:35723742
Molecular Structure-Based Screening of the Constituents of Calotropis procera Identifies Potential Inhibitors of Diabetes Mellitus Target Alpha Glucosidase. PMID:35723349
Bioinformatics and System Biology Approach to Reveal the Interaction Network and the Therapeutic Implications for Non-Small Cell Lung Cancer Patients With COVID-19. PMID:35721149
Multi-type feature fusion based on graph neural network for drug-drug interaction prediction. PMID:35689200
CDCDB: A large and continuously updated drug combination database. PMID:35654801
MSNovelist: de novo structure generation from mass spectra. PMID:35637304
In Search of Synergistic Insect Repellents: Modeling of Muscarinic GPCR Interactions with Classical and Bitopic Photoactive Ligands. PMID:35630759
BioChemDDI: Predicting Drug-Drug Interactions by Fusing Biochemical and Structural Information through a Self-Attention Mechanism. PMID:35625486
Synergistic Antifungal Activity of Synthetic Peptides and Antifungal Drugs against Candida albicans and C. parapsilosis Biofilms. PMID:35625197
In silico and in vitro study of Mycobacterium tuberculosis H37Rv uncharacterized protein (RipD): an insight on tuberculosis therapeutics. PMID:35624324
Setomimycin as a potential molecule for COVID‑19 target: in silico approach and in vitro validation. PMID:35622309
Mechanism of Fructus Mume Pills Underlying Their Protective Effects in Rats with Acetic Acid-Inducedulcerative Colitis via the Regulation of Inflammatory Cytokines and the VEGF-PI3K/Akt-eNOS Signaling Pathway. PMID:35620404
Integrated bioinformatics and statistical approaches to explore molecular biomarkers for breast cancer diagnosis, prognosis and therapies. PMID:35617355
The LOTUS initiative for open knowledge management in natural products research. PMID:35616633
Dataset of solution-based inorganic materials synthesis procedures extracted from the scientific literature. PMID:35614129
Identification of Alkaloids from Terminalia chebula as Potent SARS- CoV-2 Main Protease Inhibitors: An In Silico Perspective. PMID:35600910
An updated database of human maximum skin fluxes and epidermal permeability coefficients for drugs, xenobiotics, and other solutes applied as aqueous solutions. PMID:35599823
Exploration of the System-Level Mechanisms of the Herbal Drug FDY003 for Pancreatic Cancer Treatment: A Network Pharmacological Investigation. PMID:35591866
RHAMNETIN IS A BETTER INHIBITOR OF SARS-COV-2 2'-O-METHYLTRANSFERASE THAN DOLUTEGRAVIR: A COMPUTATIONAL PREDICTION. PMID:35582066
Molecular mechanism of ovarian toxicity of Hook.F. a study based on network pharmacology and molecular docking. PMID:35576115
Exploring Molecular Mechanisms of Aloe barbadmsis Miller on Diphenoxylate-Induced Constipation in Mice. PMID:35571728
An Herbal Product Alleviates Bleomycin-Induced Pulmonary Fibrosis in Mice via Regulating NF-κB/TNF-α Signaling in Macrophages. PMID:35548340
Andrographolide in atherosclerosis: integrating network pharmacology and in vitro pharmacological evaluation. PMID:35543243
Study on Closely Related Citrus CMMs based on Chemometrics and Prediction of Components-Targets-Diseases Network by Ingenuity Pathway Analysis. PMID:35529921
Study on the Characteristics of Small-Molecule Kinase Inhibitors-Related Drug-Induced Liver Injury. PMID:35529445
Drug-target affinity prediction using graph neural network and contact maps. PMID:35517730
Network pharmacology combined with molecular docking to explore the potential mechanisms for the antioxidant activity of Rheum tanguticum seeds. PMID:35505340
Cation-π interactions drive hydrophobic self-assembly and aggregation of niclosamide in water. PMID:35493563
Mechanism of Jujube (Ziziphus jujuba Mill.) Fruit in the Appetite Regulation Based on Network Pharmacology and Molecular Docking Method. PMID:35480085
Conjugation of a smart polymer to doxorubicin through a pH-responsive bond for targeted drug delivery and improving drug loading on graphene oxide. PMID:35478640
An in silico pipeline for the discovery of multitarget ligands: A case study for epi-polypharmacology based on DNMT1/HDAC2 inhibition. PMID:35475037
The SARS-CoV-2 helicase as a target for antiviral therapy: Identification of potential small molecule inhibitors by in silico modelling. PMID:35462185
Conformational Changes in the BSA-LT4 Complex Induced by the Presence of Vitamins: Spectroscopic Approach and Molecular Docking. PMID:35457032
DualGCN: a dual graph convolutional network model to predict cancer drug response. PMID:35428192
Virtual screening of phytochemicals from Indian medicinal plants against the endonuclease domain of SFTS virus L polymerase. PMID:35424542
ChemTastesDB: A curated database of molecular tastants. PMID:35415670
Accurate prediction of molecular targets using a self-supervised image representation learning framework. PMID:35411337
Bioinformatics Screening of Potential Biomarkers from mRNA Expression Profiles to Discover Drug Targets and Agents for Cervical Cancer. PMID:35409328
Identification of Chemical-Disease Associations Through Integration of Molecular Fingerprint, Gene Ontology and Pathway Information. PMID:35391615
Phytochemicals-based targeting RdRp and main protease of SARS-CoV-2 using docking and steered molecular dynamic simulation: A promising therapeutic approach for Tackling COVID-19. PMID:35390745
Identification of host transcriptome-guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches. PMID:35390032
Effects of Astragalus Polysaccharides on CD8+ Tissue-Resident Memory T Cells in Mice with Herpes Simplex. PMID:35388305
Potential Therapeutic Targets of Rehmannia Formulations on Diabetic Nephropathy: A Comparative Network Pharmacology Analysis. PMID:35387335
Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat. PMID:35382133
A Comprehensive Analysis of Calmodulin-Like Proteins of Glycine max Indicates Their Role in Calcium Signaling and Plant Defense Against Insect Attack. PMID:35371141
Mechanisms of Action of a Herbal Formula Huangqi Guizhi Wuwu Tang for the Management of Post-Stroke Related Numbness and Weakness: A Computational Molecular Docking Study. PMID:35369720
Influence of Medications Containing Acid Salts on Serum Bicarbonate in CKD. PMID:35369374
Explaining and avoiding failure modes in goal-directed generation of small molecules. PMID:35365218
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
Identifying Active Substances and the Pharmacological Mechanism of Houttuynia cordata Thunb. in Treating Radiation-Induced Lung Injury Based on Network Pharmacology and Molecular Docking Verification. PMID:35360660
Target Specific Inhibition of Protein Tyrosine Kinase in Conjunction With Cancer and SARS-COV-2 by Olive Nutraceuticals. PMID:35356629
INPUT: An intelligent network pharmacology platform unique for traditional Chinese medicine. PMID:35356545
Improving Compound Activity Classification via Deep Transfer and Representation Learning. PMID:35350358
Structure-based screening of natural product libraries in search of potential antiviral drug-leads as first-line treatment to COVID-19 infection. PMID:35337962
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). PMID:35325185
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PMID:35320266
Qualitative and Quantitative Evaluation of Chemical Constituents from Shuanghuanglian Injection Using Nuclear Magnetic Resonance Spectroscopy. PMID:35309716
A multitask GNN-based interpretable model for discovery of selective JAK inhibitors. PMID:35292114
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding. PMID:35292100
Machine learning prediction of 3CLpro SARS-CoV-2 docking scores. PMID:35288359
Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing. PMID:35277538
Identification and Quantitation of Bioactive and Taste-Related Dipeptides in Low-Salt Dry-Cured Ham. PMID:35269650
HIDTI: integration of heterogeneous information to predict drug-target interactions. PMID:35260608
From Platform to Knowledge Graph: Evolution of Laboratory Automation. PMID:35252980
Unraveling the Molecular Mechanism of Recognition of Selected Next-Generation Antirheumatoid Arthritis Inhibitors by Janus Kinase 1. PMID:35224383
Biochemical and Molecular Dynamics Study of a Novel GH 43 α-l-Arabinofuranosidase/β-Xylosidase From Caldicellulosiruptor saccharolyticus DSM8903. PMID:35223784
Computational Simulations Highlight the IL2Rα Binding Potential of Polyphenol Stilbenes from Fenugreek. PMID:35209009
Rapid Screening of Lipase Inhibitors from Ophiopogonis Radix Using High-Performance Thin Layer Chromatography by Two Step Gradient Elution Combined with Bioautographic Method. PMID:35208944
Molecular docking of phenolic compounds and screening of antioxidant and antidiabetic potential of Moringa oleifera ethanolic leaves extract from Qassim region, Saudi Arabia. PMID:35197753
Network Pharmacology Integrated Molecular Docking Revealed the Mechanism of Jianpi Yiqi Taohua Decoction Against Ulcerative Colitis. PMID:35173140
A Review of Approaches for Predicting Drug-Drug Interactions Based on Machine Learning. PMID:35153767
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. PMID:35076269
Antioxidant Effects and Potential Molecular Mechanism of Action of Limonium aureum Extract Based on Systematic Network Pharmacology. PMID:35071383
Tianma Formula Alleviates Dementia via ACER2-Mediated Sphingolipid Signaling Pathway Involving Aβ. PMID:35069753
Selecting molecules with diverse structures and properties by maximizing submodular functions of descriptors learned with graph neural networks. PMID:35064170
Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I. PMID:35063503
Role of Probiotics in the Management of COVID-19: A Computational Perspective. PMID:35057455
Development and Evaluation of an In Silico Dermal Absorption Model Relevant for Children. PMID:35057066
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. PMID:35031880
Preparation, urease inhibition mechanisms, and anti-Helicobacter pylori activities of hesperetin-7-rhamnoglucoside. PMID:35024644
Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study. PMID:35011598
Integrated bioinformatics and network pharmacology to identify the therapeutic target and molecular mechanisms of Huangqin decoction on ulcerative Colitis. PMID:34997010
Network Pharmacology and Inflammatory Microenvironment Strategy Approach to Finding the Potential Target of Siraitia grosvenorii (Luo Han Guo) for Glioblastoma. PMID:34987553
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors. PMID:34977999
Machine learning prediction of antiviral-HPV protein interactions for anti-HPV pharmacotherapy. PMID:34934067
Small molecules for cell reprogramming: a systems biology analysis. PMID:34919532
Network-based identification of miRNAs and transcription factors and in silico drug screening targeting δ-secretase involved in Alzheimer's disease. PMID:34917801
pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. PMID:34901870
Modeling the Structure-Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein. PMID:34898207
Genome In Silico and In Vitro Analysis of the Probiotic Properties of a Bacterial Endophyte, Bacillus Paranthracis Strain MHSD3. PMID:34858466
Identifying the Effect of Ursolic Acid Against Triple-Negative Breast Cancer: Coupling Network Pharmacology With Experiments Verification. PMID:34858165
A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. PMID:34858137
Database resources of the national center for biotechnology information. PMID:34850941
Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. PMID:34843456
A UPLC-DAD-Based Bio-Screening Assay for the Evaluation of the Angiotensin Converting Enzyme Inhibitory Potential of Plant Extracts and Compounds: Pyrroquinazoline Alkaloids from Adhatoda vasica as a Case Study. PMID:34834066
Identification of a Chemotherapeutic Lead Molecule for the Potential Disruption of the FAM72A-UNG2 Interaction to Interfere with Genome Stability, Centromere Formation, and Genome Editing. PMID:34831023
MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data. PMID:34822401
Metabolomic and lipidomic characterization of an X-chromosome deletion disorder in neural progenitor cells by UHPLC-HRMS. PMID:34820667
Development of a chemogenomics library for phenotypic screening. PMID:34819133
Characterization of folic acid-functionalized PLA-PEG nanomicelle to deliver Letrozole: A nanoinformatics study. PMID:34812575
Novel Reagent Space: Identifying Unorderable but Readily Synthesizable Building Blocks. PMID:34795876
DeepH-DTA: Deep Learning for Predicting Drug-Target Interactions: A Case Study of COVID-19 Drug Repurposing. PMID:34786289
Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors. PMID:34768977
Img2Mol - accurate SMILES recognition from molecular graphical depictions. PMID:34760202
Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors. PMID:34733103
New tale on LianHuaQingWen: IL6R/IL6/IL6ST complex is a potential target for COVID-19 treatment. PMID:34731090
MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. PMID:34729303
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. PMID:34718737
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra. PMID:34715914
Metabolite discovery through global annotation of untargeted metabolomics data. PMID:34711973
Evaluation of quercetin as a potential β-lactamase CTX-M-15 inhibitor via the molecular docking, dynamics simulations, and MMGBSA. PMID:34707432
Screening Potential Drugs for COVID-19 Based on Bound Nuclear Norm Regularization. PMID:34691157
Evaluation of Bioactive Metabolites and Antioxidant-Rich Extracts of Amaranths with Possible Role in Pancreatic Lipase Interaction: In Silico and In Vitro Studies. PMID:34677391
Deep learning allows genome-scale prediction of Michaelis constants from structural features. PMID:34665809
Quantitative prediction model for affinity of drug-target interactions based on molecular vibrations and overall system of ligand-receptor. PMID:34649499
Exploring the Mechanism of Resveratrol in Reducing the Soft Tissue Damage of Osteoarthritis Based on Network Pharmacology and Experimental Pharmacology. PMID:34646331
Integrated Network Pharmacology Analysis and In Vitro Validation Revealed the Potential Active Components and Underlying Mechanistic Pathways of Herba Patriniae in Colorectal Cancer. PMID:34641576
Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS-CoV-2 Main Protease. PMID:34633768
A case of venlafaxine-induced angioedema in an older adult. PMID:34616557
Targeting cathepsins: A potential link between COVID-19 and associated neurological manifestations. PMID:34604555
Biofluid Metabolomics of Mice Exposed to External Low-Dose Rate Radiation in a Novel Irradiation System, the Variable Dose-Rate External 137Cs Irradiator. PMID:34585931
BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes. PMID:34581602
Compound Prioritization through Meta-Analysis Enhances the Discovery of Antimicrobial Hits against Bacterial Pathogens. PMID:34572646
Inclusion of Levodopa into β-Cyclodextrin: A Comprehensive Computational Study. PMID:34568661
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. PMID:34563271
Discovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches. PMID:34560325
Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA. PMID:34548010
A cross-study analysis of drug response prediction in cancer cell lines. PMID:34524425
Ugonin J Acts as a SARS-CoV-2 3C-like Protease Inhibitor and Exhibits Anti-inflammatory Properties. PMID:34512347
SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures. PMID:34507532
In silico prediction, characterization and molecular docking studies on Glutathione-S-transferase as a molecular sieve for toxic agrochemicals explored in survey of North Indian farmers. PMID:34504970
The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. PMID:34504503
Accelerating antibiotic discovery through artificial intelligence. PMID:34504303
Anthraquinolone and quinolizine derivatives as an alley of future treatment for COVID-19: an in silico machine learning hypothesis. PMID:34504128
Supramolecular Atropine Potentiometric Sensor. PMID:34502770
Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations. PMID:34502033
Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites. PMID:34487274
Novel Butein Derivatives Repress DDX3 Expression by Inhibiting PI3K/AKT Signaling Pathway in MCF-7 and MDA-MB-231 Cell Lines. PMID:34485148
Exploring the Biological Mechanism of Huang Yam in Treating Tumors and Preventing Antitumor Drug-Induced Cardiotoxicity Using Network Pharmacology and Molecular Docking Technology. PMID:34484411
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
Machine learning methods, databases and tools for drug combination prediction. PMID:34477201
A review on machine learning approaches and trends in drug discovery. PMID:34471498
Targeting Cellular DNA Damage Responses in Cancer: An In Vitro-Calibrated Agent-Based Model Simulating Monolayer and Spheroid Treatment Responses to ATR-Inhibiting Drugs. PMID:34459993
Multi-Tissue Transcriptomic-Informed In Silico Investigation of Drugs for the Treatment of Dengue Fever Disease. PMID:34452405
Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses. PMID:34452144
SAG-DTA: Prediction of Drug-Target Affinity Using Self-Attention Graph Network. PMID:34445696
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer's Disease: Computational Refining and Biochemical Evaluation. PMID:34440715
Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery. PMID:34435882
Z-matrix template-based substitution approach for enumeration of 3D molecular structures. PMID:34430311
Classic Pentachlorophenol Hydroxylating Phenylalanine 4-Monooxygenase from Indigenous Bacillus tropicus Strain AOA-CPS1: Cloning, Overexpression, Purification, Characterization and Structural Homology Modelling. PMID:34417677
DECIMER 1.0: deep learning for chemical image recognition using transformers. PMID:34404468
In vivo and in silico studies of Dennettia tripetala essential oil reveal the potential harmful effects of habitual consumption of the plant seed. PMID:34401359
Molecular docking of alkaloid compounds with the matrix metalloproteinase 2. PMID:34393438
Computational studies reveal Fluorine based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly. PMID:34393265
Ab Initio Machine Learning in Chemical Compound Space. PMID:34387476
Investigating the Mechanism of Scutellariae barbata Herba in the Treatment of Colorectal Cancer by Network Pharmacology and Molecular Docking. PMID:34381520
Singlet-Oxygen-Induced Phospholipase A2 Inhibition: A Major Role for Interfacial Tryptophan Dioxidation. PMID:34375468
Exploring Chemical Information in PubChem. PMID:34370395
COVID-19: Vaccine Delivery System, Drug Repurposing and Application of Molecular Modeling Approach. PMID:34366663
Prediction of Drug-Induced Liver Toxicity Using SVM and Optimal Descriptor Sets. PMID:34360838
An extended reconstruction of human gut microbiota metabolism of dietary compounds. PMID:34354065
Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds. PMID:34350931
Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome. PMID:34350693
Machine-learning-accelerated multimodal characterization and multiobjective design optimization of natural porous materials. PMID:34349900
Composition of the Essential Oil Thymus schimperi and Evaluation of Its Acute and Subacute Toxicity in Wistar Albino Rats: In Silico Toxicity Studies. PMID:34349824
Phytochemical Profiling in Conjunction with In Vitro and In Silico Studies to Identify Human α-Amylase Inhibitors in Leucaena leucocephala (Lam.) De Wit for the Treatment of Diabetes Mellitus. PMID:34337243
Impact of Weaning and Maternal Immune Activation on the Metabolism of Pigs. PMID:34336923
Hydralazine augmented ultrasound hyperthermia for the treatment of hepatocellular carcinoma. PMID:34330960
Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 MPRO. PMID:34326429
Discovering and Summarizing Relationships Between Chemicals, Genes, Proteins, and Diseases in PubChem. PMID:34322655
Baicalin Rescues Cognitive Dysfunction, Mitigates Neurodegeneration, and Exerts Anti-Epileptic Effects Through Activating TLR4/MYD88/Caspase-3 Pathway in Rats. PMID:34321866
Potential drugs against COVID-19 revealed by gene expression profile, molecular docking and molecular dynamic simulation. PMID:34306168
Exploring Phytochemicals of Traditional Medicinal Plants Exhibiting Inhibitory Activity Against Main Protease, Spike Glycoprotein, RNA-dependent RNA Polymerase and Non-Structural Proteins of SARS-CoV-2 Through Virtual Screening. PMID:34305589
In silico investigation to identify potential small molecule inhibitors of the RNA-dependent RNA polymerase (RdRp) nidovirus RdRp-associated nucleotidyltransferase domain. PMID:34305155
Prophylactic treatment with BX795 blocks activation of AKT and its downstream targets to protect vaginal keratinocytes and vaginal epithelium from HSV-2 infection. PMID:34303747
Ligand-directed bias of G protein signaling at the dopamine D2 receptor. PMID:34302750
Detection of structural and conformational changes in ALS-causing mutant profilin-1 with hydrogen/deuterium exchange mass spectrometry and bioinformatics techniques. PMID:34302583
Data-driven analysis of the number of Lennard-Jones types needed in a force field. PMID:34295996
Aspergillus niger trehalase enzyme induced morphological and protein alterations on Acanthamoeba cyst and molecular docking studies. PMID:34295046
High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra. PMID:34288660
Exploration of the molecular targets and mechanisms of suxiao xintong dropping pills for myocardial infarction by network pharmacology method. PMID:34286341
Structural binding site comparisons reveal Crizotinib as a novel LRRK2 inhibitor. PMID:34285770
Transformer-based artificial neural networks for the conversion between chemical notations. PMID:34285269
Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. PMID:34273770
PubChem Periodic Table and Element Pages: Improving Access to Information on Chemical Elements from Authoritative Sources. PMID:34268481
Novel role of the dietary flavonoid fisetin in suppressing rRNA biogenesis. PMID:34267320
Effect of dapagliflozin on diabetic patients with cardiovascular disease via MAPK signalling pathway. PMID:34258872
Safe-in-Man Broad Spectrum Antiviral Agents. PMID:34258746
Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review. PMID:34258685
Potential activity of Linezolid against SARS-CoV-2 using electronic and molecular docking study. PMID:34236527
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis. PMID:34233741
Random forest classification for predicting lifespan-extending chemical compounds. PMID:34226569
Admixture Has Shaped Romani Genetic Diversity in Clinically Relevant Variants. PMID:34220960
3CLpro and PLpro affinity, a docking study to fight COVID19 based on 900 compounds from PubChem and literature. Are there new drugs to be found? PMID:34219808
Small molecule therapeutics to destabilize the ACE2-RBD complex: A molecular dynamics study. PMID:34214539
Comparison of Antioxidant and Anticancer Properties of Soft Coral-Derived Sinularin and Dihydrosinularin. PMID:34202721
In Vitro Confirmation of Siramesine as a Novel Antifungal Agent with In Silico Lead Proposals of Structurally Related Antifungals. PMID:34201401
The Advantage of Automatic Peer-Reviewing of 13C-NMR Reference Data Using the CSEARCH-Protocol. PMID:34200052
Elucidating the Mechanism of Action of the Attributed Immunomodulatory Role of Eltrombopag in Primary Immune Thrombocytopenia: An In Silico Approach. PMID:34199099
Predictive Study of the Active Ingredients and Potential Targets of Codonopsis pilosula for the Treatment of Osteosarcoma via Network Pharmacology. PMID:34194515
Optimized SQE atomic charges for peptides accessible via a web application. PMID:34193251
Binding affinity prediction for binary drug-target interactions using semi-supervised transfer learning. PMID:34189637
Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types. PMID:34174885
Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma. PMID:34164339
BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules. PMID:34163950
L-leucine stimulation of glucose uptake and utilization involves modulation of glucose - lipid metabolic switch and improved bioenergetic homeostasis in isolated rat psoas muscle ex vivo. PMID:34152488
New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids. PMID:34151400
Binding of Per- and Polyfluoro-alkyl Substances to Peroxisome Proliferator-Activated Receptor Gamma. PMID:34151090
MolDiscovery: learning mass spectrometry fragmentation of small molecules. PMID:34140479
Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2. PMID:34136511
Graph neural network based coarse-grained mapping prediction. PMID:34123175
Potential phytochemical inhibitors of SARS-CoV-2 helicase Nsp13: a molecular docking and dynamic simulation study. PMID:34117992
Combining generative artificial intelligence and on-chip synthesis for de novo drug design. PMID:34117066
Ayurveda botanicals in COVID-19 management: An in silico multi-target approach. PMID:34115763
Identifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging. PMID:34112891
Biomarkers predictive of long-term fertility found in vaginal lipidome of gilts at weaning. PMID:34110418
Insights Into Mutations Induced Conformational Changes and Rearrangement of Fe2+ Ion in pncA Gene of Mycobacterium tuberculosis to Decipher the Mechanism of Resistance to Pyrazinamide. PMID:34095218
Integrating Study on Qualitative and Quantitative Characterization of the Major Constituents in Shuanghuanglian Injection with UHPLC/Q-Orbitrap-MS and UPLC-PDA. PMID:34094616
Neuraldecipher - reverse-engineering extended-connectivity fingerprints (ECFPs) to their molecular structures. PMID:34094299
Revealing the therapeutic targets and molecular mechanisms of emodin-treated coronavirus disease 2019 via a systematic study of network pharmacology. PMID:34088885
Effects of Curcumin and Ferulic Acid on the Folding of Amyloid-β Peptide. PMID:34068636
Vibration-based biomimetic odor classification. PMID:34059734
Ranking-Oriented Quantitative Structure-Activity Relationship Modeling Combined with Assay-Wise Data Integration. PMID:34056351
Systems Pharmacology and In Silico Docking Analysis Uncover Association of CA2, PPARG, RXRA, and VDR with the Mechanisms Underlying the Shi Zhen Tea Formula Effect on Eczema. PMID:34055023
Investigation of the Multi-Target Mechanism of Guanxin-Shutong Capsule in Cerebrovascular Diseases: A Systems Pharmacology and Experimental Assessment. PMID:34054530
DFT, molecular docking and molecular dynamics simulation studies on some newly introduced natural products for their potential use against SARS-CoV-2. PMID:34054142
Molecular mechanisms of metabotropic GABAB receptor function. PMID:34049877
Kuanxiong Aerosol () in Treatment of Angina Pectoris: A Literature Review and Network Pharmacology. PMID:34047948
An Integrated Analysis of Network Pharmacology, Molecular Docking, and Experiment Validation to Explore the New Candidate Active Component and Mechanism of Cuscutae Semen-Mori Fructus Coupled-Herbs in Treating Oligoasthenozoospermia. PMID:34040346
CyProduct: A Software Tool for Accurately Predicting the Byproducts of Human Cytochrome P450 Metabolism. PMID:34038112
Based on Network Pharmacology and Molecular Docking to Explore the Underlying Mechanism of Huangqi Gegen Decoction for Treating Diabetic Nephropathy. PMID:34035828
InChI version 1.06: now more than 99.99% reliable. PMID:34030732
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights. PMID:34019663
Evaluation of Quantitative Structure Property Relationship Algorithms for Predicting Plasma Protein Binding in Humans. PMID:34017929
Integrated bioinformatic analysis reveals the underlying molecular mechanism of and potential drugs for pulmonary arterial hypertension. PMID:34016786
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. PMID:34015823
Marine algal antagonists targeting 3CL protease and spike glycoprotein of SARS-CoV-2: a computational approach for anti-COVID-19 drug discovery. PMID:34014150
Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation. PMID:34012976
A general non-self response as part of plant immunity. PMID:34007033
Network Pharmacology-Based Investigation of the Therapeutic Mechanisms of Action of Danning Tablets in Nonalcoholic Fatty Liver Disease. PMID:33995543
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. PMID:33993214
Menthol, Nicotine, and Flavoring Content of Capsule Cigarettes in the US. PMID:33987452
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. PMID:33985583
Natural plant products as potential inhibitors of RNA dependent RNA polymerase of Severe Acute Respiratory Syndrome Coronavirus-2. PMID:33984041
Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. PMID:33975934
Pharmacological Mechanisms Underlying the Anti-asthmatic Effects of Modified Guomin Decoction Determined by Network Pharmacology and Molecular Docking. PMID:33968984
A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77. PMID:33968573
Common genetic associations between age-related diseases. PMID:33959723
The Antibacterial Activity of Crude Extracts of Secondary Metabolites from Bacterial Endophytes Associated with Dicoma anomala. PMID:33953751
SANCDB: an update on South African natural compounds and their readily available analogs. PMID:33952332
Network Pharmacology and Molecular Docking Suggest the Mechanism for Biological Activity of Rosmarinic Acid. PMID:33936238
Modelling studies reveal the importance of the C-terminal inter motif loop of NSP1 as a promising target site for drug discovery and screening of potential phytochemicals to combat SARS-CoV-2. PMID:33933885
Rules of formation of H-C-N-O compounds at high pressure and the fates of planetary ices. PMID:33931549
An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents. PMID:33927701
Alantolactone inhibits cervical cancer progression by downregulating BMI1. PMID:33927214
In Silico Exploration of the Potential Role of Acetaminophen and Pesticides in the Etiology of Autism Spectrum Disorder. PMID:33925648
A computational method for drug sensitivity prediction of cancer cell lines based on various molecular information. PMID:33914775
STOUT: SMILES to IUPAC names using neural machine translation. PMID:33906675
Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study. PMID:33896392
Network-Based Analysis of Fatal Comorbidities of COVID-19 and Potential Therapeutics. PMID:33891554
Development of the Organonitrogen Biodegradation Database: Teaching Bioinformatics and Collaborative Skills to Undergraduates during a Pandemic. PMID:33884084
BC-TFdb: a database of transcription factor drivers in breast cancer. PMID:33882119
In silico investigation of potential small molecule inhibitors of the SARS-CoV-2 nsp10-nsp16 methyltransferase complex. PMID:33850334
The Use of In Silico Tools for the Toxicity Prediction of Potential Inhibitors of SARS-CoV-2. PMID:33845649
Artificial intelligence to deep learning: machine intelligence approach for drug discovery. PMID:33844136
In silico approach to understand the epigenetic mechanism of SARS-CoV-2 and its impact on the environment. PMID:33842674
Identification of hub genes and compounds controlling ovarian cancer stem cell characteristics via stemness indices analysis. PMID:33842600
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
The identification of novel inhibitors of human angiotensin-converting enzyme 2 and main protease of Sars-Cov-2: A combination of in silico methods for treatment of COVID-19. PMID:33840836
Screening of novel alkaloid inhibitors for vascular endothelial growth factor in cancer cells: an integrated computational approach. PMID:33840170
The Exploration of Novel Pharmacophore Characteristics and Multidirectional Elucidation of Structure-Activity Relationship and Mechanism of Sesquiterpene Pyridine Alkaloids from Tripterygium Based on Computational Approaches. PMID:33833819
Virtual high throughput screening: Potential inhibitors for SARS-CoV-2 PLPRO and 3CLPRO proteases. PMID:33823185
Repurposing of approved drugs with potential to interact with SARS-CoV-2 receptor. PMID:33817352
Fenamates as Potential Therapeutics for Neurodegenerative Disorders. PMID:33809987
Chemoinformatic Screening for the Selection of Potential Senolytic Compounds from Natural Products. PMID:33809876
The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository. PMID:33808985
Two Key Amino Acids Variant of α-l-arabinofuranosidase from Bacillus subtilis Str. 168 with Altered Activity for Selective Conversion Ginsenoside Rc to Rd. PMID:33808840
SARS-CoV-2 Main Protease Active Site Ligands in the Human Metabolome. PMID:33807773
Assessing the Molecular Targets and Mode of Action of Furanone C-30 on Pseudomonas aeruginosa Quorum Sensing. PMID:33803983
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. PMID:33787872
Metabolomic Biomarkers of Healthy Dietary Patterns and Cardiovascular Outcomes. PMID:33782776
Balancing Data on Deep Learning-Based Proteochemometric Activity Classification. PMID:33779173
Maize Resistance to Stem Borers Can Be Modulated by Systemic Maize Responses to Long-Term Stem Tunneling. PMID:33777059
In silico studies reveal structural deviations of mutant profilin-1 and interaction with riluzole and edaravone in amyotrophic lateral sclerosis. PMID:33767237
Teaching Cheminformatics through a Collaborative Intercollegiate Online Chemistry Course (OLCC). PMID:33762777
Role of glioblastoma stem cells in cancer therapeutic resistance: a perspective on antineoplastic agents from natural sources and chemical derivatives. PMID:33762015
Comprehensive investigation of the clinical significance of long non-coding RNA HOXA-AS2 in acute myeloid leukemia using genome-wide RNA sequencing dataset. PMID:33754013
A small molecule compound berberine as an orally active therapeutic candidate against COVID-19 and SARS: A computational and mechanistic study. PMID:33749932
Integrating 3D structural information into systems biology. PMID:33744294
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES. PMID:33736687
Salivary β-glucosidase as a direct factor influencing the occurrence of halitosis. PMID:33732903
Biosynthesis of glyceride glycoside (nonionic surfactant) by amylosucrase, a powerful glycosyltransferase. PMID:33732517
Synergistic Network Pharmacology for Traditional Chinese Medicine Liangxue Tongyu Formula in Acute Intracerebral Hemorrhagic Stroke. PMID:33727915
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification. PMID:33726837
Non-peptide agonists and positive allosteric modulators of glucagon-like peptide-1 receptors: Alternative approaches for treatment of Type 2 diabetes. PMID:33724441
FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. PMID:33724022
Identification and validation of a prognostic signature and combination drug therapy for immunotherapy of head and neck squamous cell carcinoma. PMID:33717423
Inhibition of interferon-stimulated gene 15 and lysine 48-linked ubiquitin binding to the SARS-CoV-2 papain-like protease by small molecules: In silico studies. PMID:33716308
Drug Repurposing and Polypharmacology to Fight SARS-CoV-2 Through Inhibition of the Main Protease. PMID:33692695
Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag. PMID:33685519
Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning. PMID:33683885
An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community. PMID:33683131
Systematic insight into the active constituents and mechanism of Guiqi Baizhu for the treatment of gastric cancer. PMID:33682294
Decoding the Mechanism of Huanglian Jiedu Decoction in Treating Pneumonia Based on Network Pharmacology and Molecular Docking. PMID:33681222
Effect of Syringopicroside Extracted from Syringa oblata Lindl on the Biofilm Formation of Streptococcus suis. PMID:33673668
Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics. PMID:33671368
Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2. PMID:33669738
Multi-omic analysis of stroke recurrence in African Americans from the Vitamin Intervention for Stroke Prevention (VISP) clinical trial. PMID:33661917
Identification of Potential HCV Inhibitors Based on the Interaction of Epigallocatechin-3-Gallate with Viral Envelope Proteins. PMID:33652639
Uncovering the Anti-Lung-Cancer Mechanisms of the Herbal Drug FDY2004 by Network Pharmacology. PMID:33628308
Censoring Trace-Level Environmental Data: Statistical Analysis Considerations to Limit Bias. PMID:33625843
Evaluation of drug repositioning by molecular docking of pharmaceutical resources available in the Brazilian healthcare system against SARS-CoV-2. PMID:33623816
Efficacy and Safety of New and Emerging Drugs for COVID-19: Favipiravir and Dexamethasone. PMID:33619447
MAIP: a web service for predicting blood-stage malaria inhibitors. PMID:33618772
In silico identification of potential inhibitor for TP53-induced glycolysis and apoptosis regulator in head and neck squamous cell carcinoma. PMID:33604233
Targeting Salmonella Typhimurium Invasion and Intracellular Survival Using Pyrogallol. PMID:33603727
Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. PMID:33596235
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships. PMID:33591968
Predicting Isoform-Selective Carbonic Anhydrase Inhibitors via Machine Learning and Rationalizing Structural Features Important for Selectivity. PMID:33585783
Catalpol Protects Against Pulmonary Fibrosis Through Inhibiting TGF-β1/Smad3 and Wnt/β-Catenin Signaling Pathways. PMID:33584272
Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes. PMID:33573096
Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. PMID:33569598
Protective Role of Polyphenols in Heart Failure: Molecular Targets and Cellular Mechanisms Underlying Their Therapeutic Potential. PMID:33562294
In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces. PMID:33557749
Interaction of small molecules with the SARS-CoV-2 papain-like protease: In silico studies and in vitro validation of protease activity inhibition using an enzymatic inhibition assay. PMID:33556646
Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1. PMID:33547987
A Multi-Objective Approach for Drug Repurposing in Preeclampsia. PMID:33546161
Generative chemistry: drug discovery with deep learning generative models. PMID:33543405
The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case. PMID:33530604
Molecular dynamics study of in silico mutations in the auto-inhibitory loop of human endothelial nitric oxide synthase FMN sub-domain. PMID:33527205
Virtual screening of phytochemical compounds as potential inhibitors against SARS-CoV-2 infection. PMID:33527080
Adipose saturation reduces lipotoxic systemic inflammation and explains the obesity paradox. PMID:33514548
Curing of Cocoa Beans: Fine-Scale Monitoring of the Starter Cultures Applied and Metabolomics of the Fermentation and Drying Steps. PMID:33505385
Hesperidin Interacts With CREB-BDNF Signaling Pathway to Suppress Pentylenetetrazole-Induced Convulsions in Zebrafish. PMID:33505312
A prospective study of maternal adiposity and glycemic traits across pregnancy and mid-childhood metabolomic profiles. PMID:33504931
Identification of 37 Heterogeneous Drug Candidates for Treatment of COVID-19 via a Rational Transcriptomics-Based Drug Repurposing Approach. PMID:33504008
Exploring Novel Biologically-Relevant Chemical Space Through Artificial Intelligence: The NCATS ASPIRE Program. PMID:33501158
Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis-Lycium barbarum coupled-herbs against oligoasthenozoospermia. PMID:33500463
Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. PMID:33494351
In Silico Identification of New Targets for Diagnosis, Vaccine, and Drug Candidates against Trypanosoma cruzi. PMID:33488847
Network Pharmacology Analysis of the Therapeutic Mechanisms Underlying Beimu-Gualou Formula Activity against Bronchiectasis with In Silico Molecular Docking Validation. PMID:33488758
Active learning effectively identifies a minimal set of maximally informative and asymptotically performant cytotoxic structure-activity patterns in NCI-60 cell lines. PMID:33479700
Small Molecules to Destabilize the ACE2-RBD Complex: A Molecular Dynamics Study for Potential COVID-19 Therapeutics. PMID:33469570
Human Plasma Metabolomics for Biomarker Discovery: Targeting the Molecular Subtypes in Breast Cancer. PMID:33466323
Comprehensive computational target fishing approach to identify Xanthorrhizol putative targets. PMID:33452398
Systematic Search for SARS-CoV-2 Main Protease Inhibitors for Drug Repurposing: Ethacrynic Acid as a Potential Drug. PMID:33451132
Potential repurposing of four FDA approved compounds with antiplasmodial activity identified through proteome scale computational drug discovery and in vitro assay. PMID:33446838
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
Prediction of kinase inhibitors binding modes with machine learning and reduced descriptor sets. PMID:33436888
Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2. PMID:33432321
An open source chemical structure curation pipeline using RDKit. PMID:33431044
SYBA: Bayesian estimation of synthetic accessibility of organic compounds. PMID:33431015
rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization. PMID:33431000
GEN: highly efficient SMILES explorer using autodidactic generative examination networks. PMID:33430998
Towards reproducible computational drug discovery. PMID:33430992
Dataset's chemical diversity limits the generalizability of machine learning predictions. PMID:33430991
Industry-scale application and evaluation of deep learning for drug target prediction. PMID:33430964
Exploring the Antitumor Mechanisms of Zingiberis Rhizoma Combined with Coptidis Rhizoma Using a Network Pharmacology Approach. PMID:33426081
Profiling and analysis of chemical compounds using pointwise mutual information. PMID:33423694
Microbial production of multiple short-chain primary amines via retrobiosynthesis. PMID:33420084
An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2. PMID:33418408
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
Artificial Intelligence-Based Application to Explore Inhibitors of Neurodegenerative Diseases. PMID:33414713
Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes. PMID:33411719
Membrane Depolarization Sensitizes Pseudomonas aeruginosa Against Tannic Acid. PMID:33410955
Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components. PMID:33404064
Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learning. PMID:33403260
A Versatile Interfacial Coassembly Method for Fabrication of Tunable Silica Shells with Radially Aligned Dual Mesopores on Diverse Magnetic Core Nanoparticles. PMID:33389999
The Skin Interactome: A Holistic "Genome-Microbiome-Exposome" Approach to Understand and Modulate Skin Health and Aging. PMID:33380819
A review of optical chemical structure recognition tools. PMID:33372625
DECIMER: towards deep learning for chemical image recognition. PMID:33372621
Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay. PMID:33364229
OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. PMID:33361798
Interferon-inducer antivirals: Potential candidates to combat COVID-19. PMID:33348292
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. PMID:33347301
An Investigation of the Molecular Mechanisms Underlying the Analgesic Effect of Jakyak-Gamcho Decoction: A Network Pharmacology Study. PMID:33343676
Does tetanus vaccination contribute to reduced severity of the COVID-19 infection? PMID:33341328
Aspartame, acesulfame K and sucralose- influence on the metabolism of Escherichia coli. PMID:33336183
Compounds with Antiviral, Anti-Inflammatory and Anticancer Activity Identified in Wine from Hungary's Tokaj Region via High Resolution Mass Spectrometry and Bioinformatics Analyses. PMID:33334025
In silico Assessment of Pharmacological Profile of Low Molecular Weight Oligo-Hydroxyalkanoates. PMID:33324621
New Perspectives for Resistance to PARP Inhibitors in Triple-Negative Breast Cancer. PMID:33324554
Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies? PMID:33322568
Physiologically Based Pharmacokinetic Modeling of Metoprolol Enantiomers and α-Hydroxymetoprolol to Describe CYP2D6 Drug-Gene Interactions. PMID:33322314
Propolis Suppresses UV-Induced Photoaging in Human Skin through Directly Targeting Phosphoinositide 3-Kinase. PMID:33322005
Partitioning of Selected Anisole and Veratrole Derivatives between Water and Anionic Surfactant Micelles. PMID:33317196
Chloroform fraction of Chaetomorpha brachygona, a marine green alga from Indian Sundarbans inducing autophagy in cervical cancer cells in vitro. PMID:33311531
Integrated Bioinformatics Analysis for the Screening of Associated Pathways and Therapeutic Drugs in Coronavirus Disease 2019. PMID:33309308
Ultraprocessed foods and cardiovascular health: it's not just about the nutrients. PMID:33300033
Are losartan and imatinib effective against SARS-CoV2 pathogenesis? A pathophysiologic-based in silico study. PMID:33294307
Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. PMID:33292056
Design and Synthesis of DDR1 Inhibitors with a Desired Pharmacophore Using Deep Generative Models. PMID:33289306
Antigiardial Activity of Acetylsalicylic Acid Is Associated with Overexpression of HSP70 and Membrane Transporters. PMID:33287104
Network Pharmacology Identifies the Mechanisms of Action of Tongxie Anchang Decoction in the Treatment of Irritable Bowel Syndrome with Diarrhea Predominant. PMID:33281910
DeepPurpose: a deep learning library for drug-target interaction prediction. PMID:33275143
Acylpolyamine Mygalin as a TLR4 Antagonist Based on Molecular Docking and In Vitro Analyses. PMID:33271940
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. PMID:33264402
Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors. PMID:33256167
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. PMID:33250934
Bioassay-based Corchorus capsularis L. leaf-derived β-sitosterol exerts antileishmanial effects against Leishmania donovani by targeting trypanothione reductase. PMID:33235245
Environmental risk assessment of priority biocidal substances on Polish surface water sample. PMID:33222066
Target-Centered Drug Repurposing Predictions of Human Angiotensin-Converting Enzyme 2 (ACE2) and Transmembrane Protease Serine Subtype 2 (TMPRSS2) Interacting Approved Drugs for Coronavirus Disease 2019 (COVID-19) Treatment through a Drug-Target Interaction Deep Learning Model. PMID:33218024
A Network Pharmacology to Explore the Mechanism of Astragalus Membranaceus in the Treatment of Diabetic Retinopathy. PMID:33204295
PROMISCUOUS 2.0: a resource for drug-repositioning. PMID:33196798
Rational Drug Design for Pseudomonas aeruginosa PqsA Enzyme: An in silico Guided Study to Block Biofilm Formation. PMID:33195420
A Machine Learning Method for Drug Combination Prediction. PMID:33193585
Identification and Functional Analysis of Long Non-coding RNAs in Autism Spectrum Disorders. PMID:33193567
Repurposing existing drugs for the treatment of COVID-19/SARS-CoV-2 infection: A review describing drug mechanisms of action. PMID:33191206
Network pharmacology, molecular docking integrated surface plasmon resonance technology reveals the mechanism of Toujie Quwen Granules against coronavirus disease 2019 pneumonia. PMID:33191068
Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods. PMID:33184246
High-Throughput Screening of an FDA-Approved Drug Library Identifies Inhibitors against Arenaviruses and SARS-CoV-2. PMID:33183004
A Physiologically-Based Pharmacokinetic Model of Trimethoprim for MATE1, OCT1, OCT2, and CYP2C8 Drug-Drug-Gene Interaction Predictions. PMID:33182761
In-silico drug repurposing for targeting SARS-CoV-2 main protease (Mpro). PMID:33179568
Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.). PMID:33167859
COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics. PMID:33166390
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
PubChem in 2021: new data content and improved web interfaces. PMID:33151290
Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: computational investigation. PMID:33150860
A review on drug repurposing applicable to COVID-19. PMID:33147623
Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay. PMID:33137690
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Cross-resistance of cisplatin selected cells to anti-microtubule agents: Role of general survival mechanisms. PMID:33129114
Evaluating the Association between Contrast Medium Dosage and Acute Kidney Injury in Transcatheter Aortic Valve Replacement Using Different Predictive Models. PMID:33126601
Direct 3D Printing of Silica Doped Transparent Magnesium Aluminate Spinel Ceramics. PMID:33126542
In crystallo screening for proline analog inhibitors of the proline cycle enzyme PYCR1. PMID:33109600
Sixty-One Volatiles Have Phylogenetic Signals Across Bacterial Domain and Fungal Kingdom. PMID:33101231
Reversal of Ovarian Cancer Cell Lines Multidrug Resistance Phenotype by the Association of Apiole with Chemotherapies. PMID:33096917
Database resources of the National Center for Biotechnology Information. PMID:33095870
Anti-staphylococcal activity and mode of action of thioridazine photoproducts. PMID:33093568
Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant-derived antiviral compounds. PMID:33073712
Selenium transport and metabolism in plants: Phytoremediation and biofortification implications. PMID:33068997
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. PMID:33068433
Computational Approaches in Preclinical Studies on Drug Discovery and Development. PMID:33062633
StreptomeDB 3.0: an updated compendium of streptomycetes natural products. PMID:33051671
Bayogenin 3-O-cellobioside confers non-cultivar-specific defence against the rice blast fungus Pyricularia oryzae. PMID:33043566
Resveratrol suppresses the growth and metastatic potential of cervical cancer by inhibiting STAT3Tyr705 phosphorylation. PMID:33040485
DockCoV2: a drug database against SARS-CoV-2. PMID:33035337
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PROTAC-DB: an online database of PROTACs. PMID:33010159
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CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
Unsupervised Learning and Multipartite Network Models: A Promising Approach for Understanding Traditional Medicine. PMID:32982738
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Cholinergic syndrome: a case report of acute organophosphate and carbamate poisoning. PMID:32975104
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Molecular dynamics simulation of docking structures of SARS-CoV-2 main protease and HIV protease inhibitors. PMID:32863430
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Microbial natural product databases: moving forward in the multi-omics era. PMID:32856641
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Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. PMID:32853525
The P2X7 Receptor: Central Hub of Brain Diseases. PMID:32848594
In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection. PMID:32842606
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Relevant Features of Polypharmacologic Human-Target Antimicrobials Discovered by Machine-Learning Techniques. PMID:32825532
How machine learning can help select capping layers to suppress perovskite degradation. PMID:32820159
Defining the nutritional input for genome-scale metabolic models: A roadmap. PMID:32797084
A Mechanism-Based Targeted Screen To Identify Epstein-Barr Virus-Directed Antiviral Agents. PMID:32796077
Understanding the diversity of the metal-organic framework ecosystem. PMID:32792486
Construct a circRNA/miRNA/mRNA regulatory network to explore potential pathogenesis and therapy options of clear cell renal cell carcinoma. PMID:32788609
Dual Substrate Specificity of the Rutinosidase from Aspergillus niger and the Role of Its Substrate Tunnel. PMID:32784723
Modelling, docking and simulation analysis of Bisphenol A interaction with laccase from Trichoderma. PMID:32773992
Potential mechanism prediction of Cold-Damp Plague Formula against COVID-19 via network pharmacology analysis and molecular docking. PMID:32754224
Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA-dependent RNA polymerase (RdRp) inhibition: an in-silico analysis. PMID:32720577
Pseudouridine as a novel biomarker in prostate cancer. PMID:32712138
Quantum chemical calculations for over 200,000 organic radical species and 40,000 associated closed-shell molecules. PMID:32694541
Mechanisms of Spica Prunellae against thyroid-associated Ophthalmopathy based on network pharmacology and molecular docking. PMID:32689994
Comparative Assessment of Protein Kinase Inhibitors in Public Databases and in PKIDB. PMID:32679723
A drug-biomarker interaction model to predict the key targets of Scutellaria barbata D. Don in adverse-risk acute myeloid leukaemia. PMID:32676746
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing. PMID:32657387
Small angle X-ray scattering and molecular dynamic simulations provide molecular insight for stability of recombinant human transferrin. PMID:32647821
Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLpro targeting repurposed drug candidates. PMID:32646487
Chemical, Physical and Biological Triggers of Evolutionary Conserved Bcl-xL-Mediated Apoptosis. PMID:32630560
Green synthesis of conductive polyaniline by Trametes versicolor laccase using a DNA template. PMID:32625038
Signature-based approaches for informed drug repurposing: targeting CNS disorders. PMID:32604402
Homology Modeling of Leishmanolysin (gp63) from Leishmania panamensis and Molecular Docking of Flavonoids. PMID:32596611
Exploring the Regulation Mechanism of Xihuang Pill, Olibanum and β-Boswellic Acid on the Biomolecular Network of Triple-Negative Breast Cancer Based on Transcriptomics and Chemical Informatics Methodology. PMID:32595497
Revisiting Five Years of CASMI Contests with EPA Identification Tools. PMID:32585902
ACD: Antimicrobial chemotherapeutics database. PMID:32584882
Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement. PMID:32575564
Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics. PMID:32567501
FOBI: an ontology to represent food intake data and associate it with metabolomic data. PMID:32556148
Anthelmintic drug discovery: target identification, screening methods and the role of open science. PMID:32550933
Profiling of Volatile Organic Compounds in Wild Indigenous Medicinal Ginger (Zingiber barbatum Wall.) from Myanmar. PMID:32549365
Network Pharmacology and Experimental Evidence Reveal Dioscin Suppresses Proliferation, Invasion, and EMT via AKT/GSK3b/mTOR Signaling in Lung Adenocarcinoma. PMID:32546976
Potential Antiviral Options against SARS-CoV-2 Infection. PMID:32545799
Machine Learning Applications for Mass Spectrometry-Based Metabolomics. PMID:32545768
QSRR Automator: A Tool for Automating Retention Time Prediction in Lipidomics and Metabolomics. PMID:32526851
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Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots. PMID:32490863
Nontargeted Analysis Strategy for the Identification of Phenolic Compounds in Complex Technical Lignin Samples. PMID:32468723
Structure-based drug repositioning explains ibrutinib as VEGFR2 inhibitor. PMID:32459810
TCP1γ Subunit Is Indispensable for Growth and Infectivity of Leishmania donovani. PMID:32457112
Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds. PMID:32455534
Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches. PMID:32448034
SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology. PMID:32442307
A self-adhesive microneedle patch with drug loading capability through swelling effect. PMID:32440562
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. PMID:32421831
Cannabis Constituents and Acetylcholinesterase Interaction: Molecular Docking, In Vitro Studies and Association with CNR1 rs806368 and ACHE rs17228602. PMID:32414087
Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost. PMID:32393773
Repurposing of chloroquine and some clinically approved antiviral drugs as effective therapeutics to prevent cellular entry and replication of coronavirus. PMID:32375574
Chemical Inhibitors of a Selective SWI/SNF Function Synergize with ATR Inhibition in Cancer Cell Killing. PMID:32369697
Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands. PMID:32368908
Pharmacological (or Synthetic) and Nutritional Agonists of PPAR-γ as Candidates for Cytokine Storm Modulation in COVID-19 Disease. PMID:32365556
Structure-Based Screening of Non-β-Lactam Inhibitors against Class D β-Lactamases: An Approach of Docking and Molecular Dynamics. PMID:32363287
Chemical composition and pharmacological mechanism of Qingfei Paidu Decoction and Ma Xing Shi Gan Decoction against Coronavirus Disease 2019 (COVID-19): In silico and experimental study. PMID:32360484
Drug Research Meets Network Science: Where Are We? PMID:32338900
Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. PMID:32329408
A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory. PMID:32326248
In Silico Screening for Novel Leucine Aminopeptidase Inhibitors with 3,4-Dihydroisoquinoline Scaffold. PMID:32290229
Metabolomics Adaptation of Juvenile Pacific Abalone Haliotis discus hannai to Heat Stress. PMID:32286374
Synergistic Effect of Chlorogenic Acid and Caffeic Acid with Fosfomycin on Growth Inhibition of a Resistant Listeria monocytogenes Strain. PMID:32280897
Nanoparticle Drug Delivery Systems for α-Mangostin. PMID:32280205
Hierarchical clustering of MS/MS spectra from the firefly metabolome identifies new lucibufagin compounds. PMID:32269256
Quantum Chemical Lipophilicities of Antimalarial Drugs in Relation to Terminal Half-Life. PMID:32258886
Influence of pH, temperature, and light on the stability of melatonin in aqueous solutions and fruit juices. PMID:32258489
Mechanism of rutin mediated inhibition of insulin amyloid formation and protection of Neuro-2a cells from fibril-induced apoptosis. PMID:32240467
MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action. PMID:32237745
Effect of episomally encoded DNA polymerases on chemically induced mutagenesis at the hisG46 target in Ames test. PMID:32211083
Partial Least Square Model (PLS) as a Tool to Predict the Diffusion of Steroids Across Artificial Membranes. PMID:32197506
Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. PMID:32192169
Prediction of Side Effects Using Comprehensive Similarity Measures. PMID:32190647
Translating traditional herbal formulas into modern drugs: a network-based analysis of Xiaoyao decoction. PMID:32190105
The Impact of Natural Compounds on S-Shaped Aβ42 Fibril: From Molecular Docking to Biophysical Characterization. PMID:32188076
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. PMID:32187356
Reveals of New Candidate Active Components in Hemerocallis Radix and Its Anti-Depression Action of Mechanism Based on Network Pharmacology Approach. PMID:32182911
New markers for sepsis caused by Pseudomonas aeruginosa during burn infection. PMID:32170472
GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. PMID:32164553
Clinical Pharmacology of Janus Kinase Inhibitors in Inflammatory Bowel Disease. PMID:32160283
A Network-Based Approach to Explore the Mechanisms of Uncaria Alkaloids in Treating Hypertension and Alleviating Alzheimer's Disease. PMID:32143538
The Pyrazolo[3,4-d]pyrimidine Derivative, SCO-201, Reverses Multidrug Resistance Mediated by ABCG2/BCRP. PMID:32143347
Automated recognition of functional compound-protein relationships in literature. PMID:32126064
Structure-based discovery of potent and selective melatonin receptor agonists. PMID:32118583
Trends in Helicobacter pylori resistance to clarithromycin: from phenotypic to genomic approaches. PMID:32118532
Push It to the Limit: Identification of Novel Amino Acid Changes on the Acetolactate Synthase Enzyme of Rice That Putatively Confer High Level of Tolerance to Different Imidazolinones. PMID:32117948
A Pilot Study of All-Computational Drug Design Protocol-From Structure Prediction to Interaction Analysis. PMID:32117898
Exploration of the Molecular Mechanism of FUZI (Aconiti Lateralis Radix Praeparata) in Allergic Rhinitis Treatment Based on Network Pharmacology. PMID:32114589
User guide for the discovery of potential drugs via protein structure prediction and ligand docking simulation. PMID:32108318
Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network Analysis. PMID:32085470
Discovery and development of safe-in-man broad-spectrum antiviral agents. PMID:32081774
Consensus versus Individual QSARs in Classification: Comparison on a Large-Scale Case Study. PMID:32073844
Review of the environmental prenatal exposome and its relationship to maternal and fetal health. PMID:32061676
Alterations and molecular targeting of the GSK-3 regulator, PI3K, in head and neck cancer. PMID:32061630
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. PMID:32050592
Is There a Role for Dual PI3K/mTOR Inhibitors for Patients Affected with Lymphoma? PMID:32033478
Artificial intelligence and big data facilitated targeted drug discovery. PMID:32030204
The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacology. PMID:32020584
Machine learning decodes chemical features to identify novel agonists of a moth odorant receptor. PMID:32015393
SAMPL6 logP challenge: machine learning and quantum mechanical approaches. PMID:32002780
Evidence-Based Network Approach to Recommending Targeted Cancer Therapies. PMID:31990579
Crowd-Sourced Chemistry: Considerations for Building a Standardized Database to Improve Omic Analyses. PMID:31984253
Hepatotoxicity Modeling Using Counter-Propagation Artificial Neural Networks: Handling an Imbalanced Classification Problem. PMID:31979300
The exposome and health: Where chemistry meets biology. PMID:31974245
Tracking complex mixtures of chemicals in our changing environment. PMID:31974244
In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs. PMID:31970149
In silico MS/MS spectra for identifying unknowns: a critical examination using CFM-ID algorithms and ENTACT mixture samples. PMID:31965249
Open Data for Differential Network Analysis in Glioma. PMID:31952211
Genotoxic and Carcinogenic Potential of Compounds Associated with Electronic Cigarettes: A Systematic Review. PMID:31950030
Deciphering the enzymatic target of a new family of antischistosomal agents bearing a quinazoline scaffold using complementary computational tools. PMID:31939312
Characterization of Lead Compounds Targeting the Selenoprotein Thioredoxin Glutathione Reductase for Treatment of Schistosomiasis. PMID:31939288
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Heritability estimates for 361 blood metabolites across 40 genome-wide association studies. PMID:31911595
Physiologically Based Pharmacokinetic Model to Support Ophthalmic Suspension Product Development. PMID:31907674
Marine Bacteria versus Microalgae: Who Is the Best for Biotechnological Production of Bioactive Compounds with Antioxidant Properties and Other Biological Applications? PMID:31905716
Machine and deep learning approaches for cancer drug repurposing. PMID:31904426
Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases. PMID:31895050
DDI-PULearn: a positive-unlabeled learning method for large-scale prediction of drug-drug interactions. PMID:31870276
Development of a cheminformatics platform for selectivity analyses of carbonic anhydrase inhibitors. PMID:31854205
A network pharmacology approach to reveal the protective mechanism of Salvia miltiorrhiza-Dalbergia odorifera coupled-herbs on coronary heart disease. PMID:31852981
A Deep Learning Model for Cell Growth Inhibition IC50 Prediction and Its Application for Gastric Cancer Patients. PMID:31842404
iQSPR in XenonPy: A Bayesian Molecular Design Algorithm. PMID:31841276
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
An Investigation into the Factors Governing Drug Absorption and Food Effect Prediction Based on Data Mining Methodology. PMID:31823145
Deep learning of pharmacogenomics resources: moving towards precision oncology. PMID:31813953
Rethinking drug design in the artificial intelligence era. PMID:31801986
Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. PMID:31797630
An Autophagy Modifier Screen Identifies Small Molecules Capable of Reducing Autophagosome Accumulation in a Model of CLN3-Mediated Neurodegeneration. PMID:31783699
BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities. PMID:31783634
Trypanocidal Mechanism of Action and in silico Studies of p-Coumaric Acid Derivatives. PMID:31775321
Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research. PMID:31749705
Drug Screen Identifies Leflunomide for Treatment of Inflammatory Bowel Disease Caused by TTC7A Deficiency. PMID:31743734
ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user's research. PMID:31740563
Representing Multiword Chemical Terms through Phrase-Level Preprocessing and Word Embedding. PMID:31737809
ContraDRG: Automatic Partial Charge Prediction by Machine Learning. PMID:31737032
Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data. PMID:31730249
Alterations in plasma membrane ion channel structures stimulate NLRP3 inflammasome activation in APOL1 risk milieu. PMID:31714001
Deepwater Horizon oil spill exposures and neurobehavioral function in GuLF study participants. PMID:31703974
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. PMID:31691834
MetaboLights: a resource evolving in response to the needs of its scientific community. PMID:31691833
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
Norine: update of the nonribosomal peptide resource. PMID:31691799
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
FoldamerDB: a database of peptidic foldamers. PMID:31686102
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. PMID:31665441
Predicting Materials Properties with Little Data Using Shotgun Transfer Learning. PMID:31660440
Quercetin Directly Targets JAK2 and PKCδ and Prevents UV-Induced Photoaging in Human Skin. PMID:31652815
Modeling cancer drug response through drug-specific informative genes. PMID:31645597
Targeted Metabolic Profiling of Methionine Cycle Metabolites and Redox Thiol Pools in Mammalian Plasma, Cells and Urine. PMID:31635306
Evaluating Low-Cost Optical Spectrometers for the Detection of Simulated Substandard and Falsified Medicines. PMID:31617368
Text-mined dataset of inorganic materials synthesis recipes. PMID:31615989
DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data. PMID:31614716
MIBiG 2.0: a repository for biosynthetic gene clusters of known function. PMID:31612915
Guanylin, Uroguanylin and Guanylate Cyclase-C Are Expressed in the Gastrointestinal Tract of Horses. PMID:31611814
Database resources of the National Center for Biotechnology Information. PMID:31602479
Design and Selection of Novel C1s Inhibitors by In Silico and In Vitro Approaches. PMID:31600984
STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products. PMID:31589422
Identification of a Killer Toxin from Wickerhamomyces anomalus with β-Glucanase Activity. PMID:31569379
Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity. PMID:31541145
Identification of Aloperine as an anti-apoptotic Bcl2 protein inhibitor in glioma cells. PMID:31534865
Unraveling Binding Mechanism of Alzheimer's Drug Rivastigmine Tartrate with Human Transferrin: Molecular Docking and Multi-Spectroscopic Approach towards Neurodegenerative Diseases. PMID:31533274
Kinetics and Mechanism of the Antioxidant Activities of C. olitorius and V. amygdalina by Spectrophotometric and DFT Methods. PMID:31497684
Discordant Effects of Putative Lysine Acetyltransferase Inhibitors in Biochemical and Living Systems. PMID:31480793
Identification of Compounds That Interfere with High-Throughput Screening Assay Technologies. PMID:31479198
Identification of potential agents for thymoma by integrated analyses of differentially expressed tumour-associated genes and molecular docking experiments. PMID:31452699
Quantum Chemistry Insight into the Interactions Between Deep Eutectic Solvents and SO2. PMID:31443291
Flavonoid Biosynthesis Is Likely More Susceptible to Elevation and Tree Age Than Other Branch Pathways Involved in Phenylpropanoid Biosynthesis in Ginkgo Leaves. PMID:31417595
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
Reliable Target Prediction of Bioactive Molecules Based on Chemical Similarity Without Employing Statistical Methods. PMID:31404334
PUG-View: programmatic access to chemical annotations integrated in PubChem. PMID:31399858
Identifying potential novel drugs against Helicobacter pylori by targeting the essential response regulator HsrA. PMID:31383920
Artificial Intelligence for Drug Toxicity and Safety. PMID:31383376
Combined Ensemble Docking and Machine Learning in Identification of Therapeutic Agents with Potential Inhibitory Effect on Human CES1. PMID:31362390
Long-Acting Injectable Statins-Is It Time for a Paradigm Shift? PMID:31344834
In silico comparative molecular docking analysis and analysis of the anti-inflammatory mechanisms of action of tanshinone from Salvia miltiorrhiza. PMID:31316608
Molecular simulation studies on B-cell lymphoma/leukaemia 11A (BCL11A). PMID:31312380
Novel Salicylic Acid Analogs Induce a Potent Defense Response in Arabidopsis. PMID:31288496
Mapping the Site of Action of Human P2X7 Receptor Antagonists AZ11645373, Brilliant Blue G, KN-62, Calmidazolium, and ZINC58368839 to the Intersubunit Allosteric Pocket. PMID:31263019
PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands. PMID:31250014
The Consortium of Metabolomics Studies (COMETS): Metabolomics in 47 Prospective Cohort Studies. PMID:31155658
Homology modeling and site-directed mutagenesis identify amino acid residues underlying the substrate selection mechanism of human monocarboxylate transporters 1 (hMCT1) and 4 (hMCT4). PMID:31101938
In Silico Study of the Resistance to Organophosphorus Pesticides Associated with Point Mutations in Acetylcholinesterase of Lepidoptera: B. mandarina, B. mori, C. auricilius, C. suppressalis, C. pomonella, H. armígera, P. xylostella, S. frugiperda, and S. litura. PMID:31096579
Marine Natural Products from Microalgae: An -Omics Overview. PMID:31067655
DrugComb: an integrative cancer drug combination data portal. PMID:31066443
Quercetin conjugated with superparamagnetic iron oxide nanoparticles improves learning and memory better than free quercetin via interacting with proteins involved in LTP. PMID:31053743
A Bioinformatics View of Glycan⁻Virus Interactions. PMID:31018588
Late Neurological Consequences of Zika Virus Infection: Risk Factors and Pharmaceutical Approaches. PMID:30999590
Linking Bisphenol S to Adverse Outcome Pathways Using a Combined Text Mining and Systems Biology Approach. PMID:30994381
Labellum structure of Bulbophyllum echinolabium J.J. Sm. (section Lepidorhiza Schltr., Bulbophyllinae Schltr., Orchidaceae Juss.). PMID:30993470
Marine macroalga Caulerpa: role of its metabolites in modulating cancer signaling. PMID:30980271
SugarSketcher: Quick and Intuitive Online Glycan Drawing. PMID:30563078
PubChem: a public information system for analyzing bioactivities of small molecules PubMed citations: 442.

442 articles citing: PubChem: a public information system for analyzing bioactivities of small molecules

Insight into the Structure-Odor Relationship of Molecules: A Computational Study Based on Deep Learning. PMID:35885276
Molecular docking analysis and evaluation of the antimicrobial properties of the constituents of Geranium wallichianum D. Don ex Sweet from Kashmir Himalaya. PMID:35869098
Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Berberine in the Treatment of Ischaemic Stroke. PMID:35815278
Artificial intelligence in cancer target identification and drug discovery. PMID:35538061
Predicting Prenatal Developmental Toxicity Based On the Combination of Chemical Structures and Biological Data. PMID:35451820
PIGNet: a physics-informed deep learning model toward generalized drug-target interaction predictions. PMID:35432900
Integration of Neighbor Topologies Based on Meta-Paths and Node Attributes for Predicting Drug-Related Diseases. PMID:35409235
PSRR: A Web Server for Predicting the Regulation of miRNAs Expression by Small Molecules. PMID:35386297
Unveiling Potential Mechanisms of Spatholobi Caulis against Lung Metastasis of Malignant Tumor by Network Pharmacology and Molecular Docking. PMID:35356244
Evaluation of Blood-Brain-Barrier Permeability, Neurotoxicity, and Potential Cognitive Impairment by Pseudomonas aeruginosa's Virulence Factor Pyocyanin. PMID:35340215
Interaction Analysis of MRP1 with Anticancer Drugs Used in Ovarian Cancer: In Silico Approach. PMID:35330134
High-Throughput Screening Assay Profiling for Large Chemical Databases. PMID:35294761
Cell cycle arrest is an important mechanism of action of compound Kushen injection in the prevention of colorectal cancer. PMID:35288618
An Integrated Pharmacology-Based Strategy to Investigate the Potential Mechanism of Xiebai San in Treating Pediatric Pneumonia. PMID:35237157
A network pharmacology-based approach to explore mechanism of action of medicinal herbs for alopecia treatment. PMID:35181715
Hepatoprotective mechanism of Silybum marianum on nonalcoholic fatty liver disease based on network pharmacology and experimental verification. PMID:35170400
A deep-learning system bridging molecule structure and biomedical text with comprehension comparable to human professionals. PMID:35165275
MiRNA-Drug Resistance Association Prediction Through the Attentive Multimodal Graph Convolutional Network. PMID:35095506
Identification of miRNA-Small Molecule Associations by Continuous Feature Representation Using Auto-Encoders. PMID:35056899
Artificial intelligence: machine learning for chemical sciences. PMID:34955617
Molecular Docking Simulation Studies Identifies Potential Natural Product Derived-Antiwolbachial Compounds as Filaricides against Onchocerciasis. PMID:34829911
DaiCee: A database for anti-cancer compounds with targets and side effect profiles. PMID:34803258
Multivariate classification techniques and mass spectrometry as a tool in the screening of patients with fibromyalgia. PMID:34799667
Exploring the mechanism of Yixinyin for myocardial infarction by weighted co-expression network and molecular docking. PMID:34799616
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion. PMID:34717542
Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches. PMID:34681845
Sequence Engineering of an Aspergillus niger Tannase to Produce in Pichia pastoris a Single-Chain Enzyme with High Specific Activity. PMID:34655039
Exploring the Molecular Mechanism of Astragali Radix-Curcumae Rhizoma against Gastric Intraepithelial Neoplasia by Network Pharmacology and Molecular Docking. PMID:34646329
Exploring and mapping chemical space with molecular assembly trees. PMID:34559562
Web-Based Quantitative Structure-Activity Relationship Resources Facilitate Effective Drug Discovery. PMID:34554348
In silico prediction of natural compounds as potential multi-target inhibitors of structural proteins of SARS-CoV-2. PMID:34486935
Insights into the molecular mechanisms of Huangqi decoction on liver fibrosis via computational systems pharmacology approaches. PMID:34301291
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Aspergillus Metabolome Database for Mass Spectrometry Metabolomics. PMID:34063531
Carnosol Is a Novel Inhibitor of p300 Acetyltransferase in Breast Cancer. PMID:34055630
An Integrated Analysis of Network Pharmacology, Molecular Docking, and Experiment Validation to Explore the New Candidate Active Component and Mechanism of Cuscutae Semen-Mori Fructus Coupled-Herbs in Treating Oligoasthenozoospermia. PMID:34040346
An Ensemble Learning-Based Method for Inferring Drug-Target Interactions Combining Protein Sequences and Drug Fingerprints. PMID:33987446
In Silico Identification of Small Molecules as New Cdc25 Inhibitors through the Correlation between Chemosensitivity and Protein Expression Pattern. PMID:33918281
Comparative transcriptomics and network pharmacology analysis to identify the potential mechanism of celastrol against osteoarthritis. PMID:33870466
Comprehensive investigation of the clinical significance of long non-coding RNA HOXA-AS2 in acute myeloid leukemia using genome-wide RNA sequencing dataset. PMID:33754013
An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community. PMID:33683131
Applying regulatory science in traditional chinese medicines for improving public safety and facilitating innovation in China: a scoping review and regulatory implications. PMID:33593397
Catechin as the Most Efficient Bioactive Compound from Azadirachta indica with Antibiofilm and Anti-quorum Sensing Activities Against Dental Biofilm: an In Vitro and In Silico Study. PMID:33496925
EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation. PMID:33431049
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. PMID:33431021
Dataset's chemical diversity limits the generalizability of machine learning predictions. PMID:33430991
Learning important features from multi-view data to predict drug side effects. PMID:33430979
Attenuation of Pseudomonas aeruginosa biofilm by thymoquinone: an individual and combinatorial study with tetrazine-capped silver nanoparticles and tryptophan. PMID:33411249
Differential Effects of IGF-1R Small Molecule Tyrosine Kinase Inhibitors BMS-754807 and OSI-906 on Human Cancer Cell Lines. PMID:33322337
Mapping Chemical Respiratory Sensitization: How Useful Are Our Current Computational Tools? PMID:33320000
3,4-dihydroxytoluene, a metabolite of rutin, suppresses the progression of nonalcoholic fatty liver disease in mice by inhibiting p300 histone acetyltransferase activity. PMID:33303988
Parthenolide inhibits the growth of non-small cell lung cancer by targeting epidermal growth factor receptor. PMID:33292235
Hydroxylated Chalcones as Aryl Hydrocarbon Receptor Agonists: Structure-Activity Effects. PMID:33263770
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. PMID:33245774
H-RACS: a handy tool to rank anti-cancer synergistic drugs. PMID:33173014
Insights into the mechanism of Arnebia euchroma on leukemia via network pharmacology approach. PMID:33109189
Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches. PMID:33076254
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction. PMID:33070179
Virtual Screening Technique Used to Estimate the Mechanism of Adhatoda vasica Nees for the Treatment of Rheumatoid Arthritis Based on Network Pharmacology and Molecular Docking. PMID:33062015
Circulating Metabolites as Potential Biomarkers for Neurological Disorders-Metabolites in Neurological Disorders. PMID:33003305
New developments in RiPP discovery, enzymology and engineering. PMID:32935693
A narrative literature review on traditional medicine options for treatment of corona virus disease 2019 (COVID-19). PMID:32891290
A Metabolomics Workflow for Analyzing Complex Biological Samples Using a Combined Method of Untargeted and Target-List Based Approaches. PMID:32854199
In silico analyzing the molecular interactions of plant-derived inhibitors against E6AP, p53, and c-Myc binding sites of HPV type 16 E6 oncoprotein. PMID:32802901
Generative Model for Proposing Drug Candidates Satisfying Anticancer Properties Using a Conditional Variational Autoencoder. PMID:32775866
Mechanism of Astragalus membranaceus in the treatment of laryngeal cancer based on gene co-expression network and molecular docking. PMID:32636440
Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models. PMID:32601839
A Novel Triple Matrix Factorization Method for Detecting Drug-Side Effect Association Based on Kernel Target Alignment. PMID:32596314
Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement. PMID:32575564
Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study. PMID:32573355
Leishmanicidal Potential of Hardwickiic Acid Isolated From Croton sylvaticus. PMID:32523532
Dual graph convolutional neural network for predicting chemical networks. PMID:32321421
Glycosyl flavones from Humulus japonicus suppress MMP-1 production via decreasing oxidative stress in UVB irradiated human dermal fibroblasts. PMID:32317077
A deep learning-based method for drug-target interaction prediction based on long short-term memory neural network. PMID:32183788
Wikidata as a knowledge graph for the life sciences. PMID:32180547
SPVec: A Word2vec-Inspired Feature Representation Method for Drug-Target Interaction Prediction. PMID:31998687
Machine-Learning-Assisted De Novo Design of Organic Molecules and Polymers: Opportunities and Challenges. PMID:31936321
DDIGIP: predicting drug-drug interactions based on Gaussian interaction profile kernels. PMID:31874609
HeteroDualNet: A Dual Convolutional Neural Network With Heterogeneous Layers for Drug-Disease Association Prediction via Chou's Five-Step Rule. PMID:31780934
SNMFSMMA: using symmetric nonnegative matrix factorization and Kronecker regularized least squares to predict potential small molecule-microRNA association. PMID:31739716
Comprehensive ensemble in QSAR prediction for drug discovery. PMID:31655545
Drug Side-Effect Prediction Via Random Walk on the Signed Heterogeneous Drug Network. PMID:31614686
Using MS-FINDER for identifying 19 natural products in the CASMI 2016 contest. PMID:31576201
The metaRbolomics Toolbox in Bioconductor and beyond. PMID:31548506
Big Data and Artificial Intelligence Modeling for Drug Discovery. PMID:31518513
Large-Scale Target Identification of Herbal Medicine Using a Reverse Docking Approach. PMID:31460061
Prediction of Potential Drug-Disease Associations through Deep Integration of Diversity and Projections of Various Drug Features. PMID:31443472
Exploring the new horizons of drug repurposing: A vital tool for turning hard work into smart work. PMID:31421629
AI in Health: State of the Art, Challenges, and Future Directions. PMID:31419814
Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit. PMID:31349692
Convolutional Neural Network and Bidirectional Long Short-Term Memory-Based Method for Predicting Drug-Disease Associations. PMID:31336774
Multi-Target β-Protease Inhibitors from Andrographis paniculata: In Silico and In Vitro Studies. PMID:31319560
Use of big data in drug development for precision medicine: an update. PMID:31286058
Molecular pharmacology of metabotropic receptors targeted by neuropsychiatric drugs. PMID:31270468
PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. PMID:31259547
Leveraging Image-Derived Phenotypic Measurements for Drug-Target Interaction Predictions. PMID:31217689
Dual binding mode of "bitter sugars" to their human bitter taste receptor target. PMID:31186454
In silico prediction of chemical aquatic toxicity for marine crustaceans via machine learning. PMID:31160968
MENDA: a comprehensive curated resource of metabolic characterization in depression. PMID:31157825
Synthesis, Biological Evaluation, and In Silico Studies of Novel Aminated Xanthones as Potential p53-Activating Agents. PMID:31121972
Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin. PMID:31048752
Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure-Activity Relationship (QSAR) Analysis. PMID:30984753
Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and Mechanism-Driven Modeling for Chemical Toxicity. PMID:30907586
Identification of pathways associated with chemosensitivity through network embedding. PMID:30893303
Phenolic Compounds Inhibit 3T3-L1 Adipogenesis Depending on the Stage of Differentiation and Their Binding Affinity to PPARγ. PMID:30884812
Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment. PMID:30846939
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. PMID:30768156
Systematic Understanding of the Mechanism of Baicalin against Ischemic Stroke through a Network Pharmacology Approach. PMID:30647760
A probabilistic molecular fingerprint for big data settings. PMID:30564943
Tannic acid, a novel histone acetyltransferase inhibitor, prevents non-alcoholic fatty liver disease both in vivo and in vitro model. PMID:30473486
Prediction of Potential Small Molecule-Associated MicroRNAs Using Graphlet Interaction. PMID:30374302
Predictive classifier models built from natural products with antimalarial bioactivity using machine learning approach. PMID:30265702
Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas. PMID:30223552
AromaDb: A Database of Medicinal and Aromatic Plant's Aroma Molecules With Phytochemistry and Therapeutic Potentials. PMID:30150996
Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers. PMID:30123424
Review of Drug Repositioning Approaches and Resources. PMID:30123072
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
In silico prediction of pesticide aquatic toxicity with chemical category approaches. PMID:30090546
Designing Algorithms To Aid Discovery by Chemical Robots. PMID:30062108
Implications of Off-Target Serotoninergic Drug Activity: An Analysis of Serotonin Syndrome Reports Using a Systematic Bioinformatics Approach. PMID:29972695
DPubChem: a web tool for QSAR modeling and high-throughput virtual screening. PMID:29904147
Metabolite extraction for high-throughput FTICR-MS-based metabolomics of grapevine leaves. PMID:29900113
High-Throughput Screening Assay Datasets from the PubChem Database. PMID:29795804
Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification. PMID:29790753
Data Mining and Computational Modeling of High-Throughput Screening Datasets. PMID:29671272
Realizing drug repositioning by adapting a recommendation system to handle the process. PMID:29649971
LipidPedia: a comprehensive lipid knowledgebase. PMID:29648583
A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration. PMID:29642848
Promises and pitfalls of untargeted metabolomics. PMID:29536203
Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening. PMID:29516311
In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts. PMID:29515993
Development of a Reverse Phase HPLC Retention Index Model for Nontargeted Metabolomics Using Synthetic Compounds. PMID:29489351
Inferences of individual drug responses across diverse cancer types using a novel competing endogenous RNA network. PMID:29464864
Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies. PMID:29464421
Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications. PMID:29442436
An automated framework for QSAR model building. PMID:29340790
A unified frame of predicting side effects of drugs by using linear neighborhood similarity. PMID:29297371
Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server. PMID:29297315
vNN Web Server for ADMET Predictions. PMID:29255418
CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. PMID:29220450
Drug-Target Interaction Prediction through Label Propagation with Linear Neighborhood Information. PMID:29186828
Are there physicochemical differences between allosteric and competitive ligands? PMID:29125840
RD-Metabolizer: an integrated and reaction types extensive approach to predict metabolic sites and metabolites of drug-like molecules. PMID:29086838
ChemSAR: an online pipelining platform for molecular SAR modeling. PMID:29086046
Exhaustive sampling of the fragment space associated to a molecule leading to the generation of conserved fragments. PMID:29063731
UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics. PMID:29040459
Tissue specificity of in vitro drug sensitivity. PMID:29016819
Drug repurposing in idiopathic pulmonary fibrosis filtered by a bioinformatics-derived composite score. PMID:28974751
Orthologue chemical space and its influence on target prediction. PMID:28961699
PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets. PMID:28931422
Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. PMID:28478508
Combined lipidomic and proteomic analysis of isolated human islets exposed to palmitate reveals time-dependent changes in insulin secretion and lipid metabolism. PMID:28448538
PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing. PMID:28346087
metaX: a flexible and comprehensive software for processing metabolomics data. PMID:28327092
Network Pharmacology Studies on the Bioactive Compounds and Action Mechanisms of Natural Products for the Treatment of Diabetes Mellitus: A Review. PMID:28280467
The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data. PMID:28270862
Insights into the molecular mechanisms of Polygonum multiflorum Thunb-induced liver injury: a computational systems toxicology approach. PMID:28239160
Novel Approach to Classify Plants Based on Metabolite-Content Similarity. PMID:28164123
Purification, Biochemical Characterization, and Amino Acid Sequence of a Novel Type of Lectin from Aplysia dactylomela Eggs with Antibacterial/Antibiofilm Potential. PMID:28150103
Global open data management in metabolomics. PMID:28092796
The Antagonistic Effect of Mycotoxins Deoxynivalenol and Zearalenone on Metabolic Profiling in Serum and Liver of Mice. PMID:28075412
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data. PMID:28056782
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. PMID:28007024
Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction. PMID:28001004
In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (Panax vietnamesis). PMID:27924272
PubChem BioAssay: 2017 update. PMID:27899599
DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning. PMID:27895719
Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets. PMID:27872662
Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach. PMID:27784988
Discovery of 8-Membered Ring Sulfonamides as Inhibitors of Oncogenic Mutant Isocitrate Dehydrogenase 1. PMID:27774134
Leveraging graph topology and semantic context for pharmacovigilance through twitter-streams. PMID:27766937
Using C. elegans Forward and Reverse Genetics to Identify New Compounds with Anthelmintic Activity. PMID:27755544
Identification of Suitable Natural Inhibitor against Influenza A (H1N1) Neuraminidase Protein by Molecular Docking. PMID:27729839
Structural insights into the polypharmacological activity of quercetin on serine/threonine kinases. PMID:27729770
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium. PMID:27686671
Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach. PMID:27594785
LigandBox: A database for 3D structures of chemical compounds. PMID:27493549
Context-specific functional module based drug efficacy prediction. PMID:27490093
DrugQuest - a text mining workflow for drug association discovery. PMID:27295093
Literature information in PubChem: associations between PubChem records and scientific articles. PMID:27293485
HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V. PMID:27270713
Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery. PMID:27234029
Identification of associations between small molecule drugs and miRNAs based on functional similarity. PMID:27232942
Lead identification for the K-Ras protein: virtual screening and combinatorial fragment-based approaches. PMID:27217775
In silico identification of anti-cancer compounds and plants from traditional Chinese medicine database. PMID:27145869
systemsDock: a web server for network pharmacology-based prediction and analysis. PMID:27131384
Acetogenins from Annona muricata as potential inhibitors of antiapoptotic proteins: a molecular modeling study. PMID:27110097
Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway. PMID:27097161
Inhibition of DNA Topoisomerase Type IIα (TOP2A) by Mitoxantrone and Its Halogenated Derivatives: A Combined Density Functional and Molecular Docking Study. PMID:27088089
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. PMID:27087307
Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics. PMID:27075578
Predicting drug target interactions using meta-path-based semantic network analysis. PMID:27071755
BitterX: a tool for understanding bitter taste in humans. PMID:27040075
Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach. PMID:27026843
DASPfind: new efficient method to predict drug-target interactions. PMID:26985240
New strategy for drug discovery by large-scale association analysis of molecular networks of different species. PMID:26912056
Supporting read-across using biological data. PMID:26863516
Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. PMID:26808821
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. PMID:26794319
COLLECTIVE PAIRWISE CLASSIFICATION FOR MULTI-WAY ANALYSIS OF DISEASE AND DRUG DATA. PMID:26776175
Prediction of disease-gene-drug relationships following a differential network analysis. PMID:26775695
Historeceptomic Fingerprints for Drug-Like Compounds. PMID:26733872
Artificial neural network cascade identifies multi-P450 inhibitors in natural compounds. PMID:26719820
Mining Chemical Activity Status from High-Throughput Screening Assays. PMID:26658480
Prediction and Characterisation of the System Effects of Aristolochic Acid: A Novel Joint Network Analysis towards Therapeutic and Toxicological Mechanisms. PMID:26620132
Database resources of the National Center for Biotechnology Information. PMID:26615191
In silico approach for the discovery of new PPARγ modulators among plant-derived polyphenols. PMID:26604687
SureChEMBL: a large-scale, chemically annotated patent document database. PMID:26582922
Predicting drug side effects by multi-label learning and ensemble learning. PMID:26537615
Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. PMID:26535158
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs. PMID:26491652
SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. PMID:26490957
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. PMID:26481362
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. PMID:26467476
The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomics. PMID:26448899
Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model. PMID:26418249
Predicting Mouse Liver Microsomal Stability with "Pruned" Machine Learning Models and Public Data. PMID:26415647
2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib. PMID:26403354
PubChem Substance and Compound databases. PMID:26400175
Identification of Novel Aldose Reductase Inhibitors from Spices: A Molecular Docking and Simulation Study. PMID:26384019
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
Screening of potential targets in Plasmodium falciparum using stage-specific metabolic network analysis. PMID:26303382
Optimizing drug-target interaction prediction based on random walk on heterogeneous networks. PMID:26300984
Computational approaches to natural product discovery. PMID:26284671
SerpentinaDB: a database of plant-derived molecules of Rauvolfia serpentina. PMID:26238452
Label Propagation Prediction of Drug-Drug Interactions Based on Clinical Side Effects. PMID:26196247
In Silico Docking to Explicate Interface between Plant-Originated Inhibitors and E6 Oncogenic Protein of Highly Threatening Human Papillomavirus 18. PMID:26175664
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites. PMID:26173699
TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine. PMID:26156871
PubChem structure-activity relationship (SAR) clusters. PMID:26150895
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily. PMID:26100629
Current Challenges in Development of a Database of Three-Dimensional Chemical Structures. PMID:26075200
Checking the STEP-Associated Trafficking and Internalization of Glutamate Receptors for Reduced Cognitive Deficits: A Machine Learning Approach-Based Cheminformatics Study and Its Application for Drug Repurposing. PMID:26066505
An Ebola virus-centered knowledge base. PMID:26055098
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. PMID:26047637
Acute Toxicity-Supported Chronic Toxicity Prediction: A k-Nearest Neighbor Coupled Read-Across Strategy. PMID:26006240
Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets. PMID:25994950
Towards drug repositioning: a unified computational framework for integrating multiple aspects of drug similarity and disease similarity. PMID:25954437
PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. PMID:25934803
ChEMBL web services: streamlining access to drug discovery data and utilities. PMID:25883136
Pharmacoinformatics approach for investigation of alternative potential hepatitis C virus nonstructural protein 5B inhibitors. PMID:25848219
Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens. PMID:25826798
An S188V mutation alters substrate specificity of non-stereospecific α-haloalkanoic acid dehalogenase E (DehE). PMID:25816329
A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature. PMID:25810779
A document processing pipeline for annotating chemical entities in scientific documents. PMID:25810778
Understanding Rifampicin Resistance in Tuberculosis through a Computational Approach. PMID:25705170
Cheminformatics models for inhibitors of Schistosoma mansoni thioredoxin glutathione reductase. PMID:25629082
Computational analysis and low-scale constitutive expression of laccases synthetic genes GlLCC1 from Ganoderma lucidum and POXA 1B from Pleurotus ostreatus in Pichia pastoris. PMID:25611746
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina. PMID:25582171
Follow up: Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer. PMID:25520777
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases. PMID:25486901
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. PMID:25477388
Comparative Structural and Functional Analysis of Staphylococcus aureus Glucokinase with other Bacterial Glucokinases. PMID:25425757
Parallel worlds of public and commercial bioactive chemistry data. PMID:25415348
Database resources of the National Center for Biotechnology Information. PMID:25398906
Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. PMID:25362883
Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level. PMID:25313158
Big data in chemical toxicity research: the use of high-throughput screening assays to identify potential toxicants. PMID:25195622
PubChem applications in drug discovery: a bibliometric analysis. PMID:25168772
Elucidating Molecular Interactions of Natural Inhibitors with HPV-16 E6 Oncoprotein through Docking Analysis. PMID:25031569
Profiling animal toxicants by automatically mining public bioassay data: a big data approach for computational toxicology. PMID:24950175
Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data. PMID:24949426
Expanding the fragrance chemical space for virtual screening. PMID:24876890
Towards structural systems pharmacology to study complex diseases and personalized medicine. PMID:24830652
Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis. PMID:24828308
An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs. PMID:24749745
Label-free drug discovery. PMID:24723889
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Computational tools for the secondary analysis of metabolomics experiments. PMID:24688685
Molpher: a software framework for systematic chemical space exploration. PMID:24655571
Structural and Functional analysis of Staphylococcus aureus NADP-dependent IDH and its comparison with Bacterial and Human NADPdependent IDH. PMID:24616559
Discovery of potent positive allosteric modulators of the α3β2 nicotinic acetylcholine receptor by a chemical space walk in ChEMBL. PMID:24593915
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. PMID:24564846
Pathway-based drug repositioning using causal inference. PMID:24564553
Interaction network among functional drug groups. PMID:24555875
Exploring the relationship between drug side-effects and therapeutic indications. PMID:24551427
A network pharmacology approach to determine active compounds and action mechanisms of ge-gen-qin-lian decoction for treatment of type 2 diabetes. PMID:24527048
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. PMID:24441647
Network understanding of herb medicine via rapid identification of ingredient-target interactions. PMID:24429698
Web search and data mining of natural products and their bioactivities in PubChem. PMID:24363665
Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications. PMID:24358818
Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease. PMID:24352679
The receptor binding domain of MERS-CoV: the dawn of vaccine and treatment development. PMID:24342026
The Transformer database: biotransformation of xenobiotics. PMID:24334957
Extending the "web of drug identity" with knowledge extracted from United States product labels. PMID:24303301
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Database resources of the National Center for Biotechnology Information. PMID:24259429
Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana. PMID:24252103
PubChem BioAssay: 2014 update. PMID:24198245
Structure and function of the Smoothened extracellular domain in vertebrate Hedgehog signaling. PMID:24171105
Lipid receptor S1P₁ activation scheme concluded from microsecond all-atom molecular dynamics simulations. PMID:24098103
GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. PMID:24078711
An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions. PMID:23951139
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. PMID:23875761
Distinct pools of non-glycolytic substrates differentiate brain regions and prime region-specific responses of mitochondria. PMID:23874783
Target essentiality and centrality characterize drug side effects. PMID:23874169
eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. PMID:23838840
Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology. PMID:23826885
The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling. PMID:23781802
Drug repurposing: mining protozoan proteomes for targets of known bioactive compounds. PMID:23757409
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
Untargeted metabolomics from biological sources using ultraperformance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS). PMID:23711563
Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PMID:23704901
Primuline derivatives that mimic RNA to stimulate hepatitis C virus NS3 helicase-catalyzed ATP hydrolysis. PMID:23703611
Tranilast binds to aβ monomers and promotes aβ fibrillation. PMID:23679559
An Integrative Platform of TCM Network Pharmacology and Its Application on a Herbal Formula, Qing-Luo-Yin. PMID:23653662
New Perspectives on How to Discover Drugs from Herbal Medicines: CAM's Outstanding Contribution to Modern Therapeutics. PMID:23634172
The MetaboLights repository: curation challenges in metabolomics. PMID:23630246
Managing missing measurements in small-molecule screens. PMID:23585219
In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life. PMID:23578025
Recent progress in the development of metabolome databases for plant systems biology. PMID:23577015
Non-target screening of veterinary drugs using tandem mass spectrometry on SmartMass. PMID:23532781
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Target identification and mechanism of action in chemical biology and drug discovery. PMID:23508189
Designing of inhibitors against drug tolerant Mycobacterium tuberculosis (H37Rv). PMID:23497593
COX-2 structural analysis and docking studies with gallic acid structural analogues. PMID:23483789
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. PMID:23482073
Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. PMID:23437217
Predictive modeling of anti-malarial molecules inhibiting apicoplast formation. PMID:23419172
iBIOMES: managing and sharing biomolecular simulation data in a distributed environment. PMID:23413948
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
Thioredoxin system: a model for determining novel lead molecules for breast cancer chemotherapy. PMID:23407461
BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space. PMID:23330685
Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis. PMID:23325804
Chapter 3: Small molecules and disease. PMID:23300405
TargetHunter: an in silico target identification tool for predicting therapeutic potential of small organic molecules based on chemogenomic database. PMID:23292636
PubChem3D: conformer ensemble accuracy. PMID:23289532
Large-scale reverse docking profiles and their applications. PMID:23282219
Database resources of the National Center for Biotechnology Information. PMID:23193264
Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). PMID:23155465
What in silico molecular docking can do for the 'bench-working biologists'. PMID:23151798
ClusterMine360: a database of microbial PKS/NRPS biosynthesis. PMID:23104377
The effect of curcumin on human bronchial epithelial cells exposed to fine particulate matter: a predictive analysis. PMID:23090021
Exploring chemical space for drug discovery using the chemical universe database. PMID:23019491
The use of glycoinformatics in glycochemistry. PMID:23015842
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
Agonistic effect of polyunsaturated fatty acids (PUFAs) and its metabolites on brain-derived neurotrophic factor (BDNF) through molecular docking simulation. PMID:22943296
An overview of computational life science databases & exchange formats of relevance to chemical biology research. PMID:22934944
Computational analysis and predictive modeling of small molecule modulators of microRNA. PMID:22889302
Profiling lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. PMID:22843995
Comparison and correlation of binding mode of ATP in the kinase domains of Hexokinase family. PMID:22829728
System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium. PMID:22787274
IUPHAR-DB: an open-access, expert-curated resource for receptor and ion channel research. PMID:22778867
Public domain databases for medicinal chemistry. PMID:22731701
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. PMID:22730453
A two-step target binding and selectivity support vector machines approach for virtual screening of dopamine receptor subtype-selective ligands. PMID:22720033
Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. PMID:22690147
Behavioral barcoding in the cloud: embracing data-intensive digital phenotyping in neuropharmacology. PMID:22652049
Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. PMID:22629264
LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. PMID:22594624
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. PMID:22591066
Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation. PMID:22587916
Surflex-Dock: Docking benchmarks and real-world application. PMID:22569590
Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis. PMID:22559876
MarVis-Filter: ranking, filtering, adduct and isotope correction of mass spectrometry data. PMID:22550397
Paradigm shift in toxicity testing and modeling. PMID:22528508
Metab2MeSH: annotating compounds with medical subject headings. PMID:22492643
Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets. PMID:22463123
In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance. PMID:22373185
Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses. PMID:22355792
Blind trials of computer-assisted structure elucidation software. PMID:22321892
Comparative modeling of PON2 and analysis of its substrate binding interactions using computational methods. PMID:22319641
A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space. PMID:22316383
Modulating protein-protein interactions with small molecules: the importance of binding hotspots. PMID:22198293
PubChem's BioAssay Database. PMID:22140110
Database resources of the National Center for Biotechnology Information. PMID:22140104
TDR Targets: a chemogenomics resource for neglected diseases. PMID:22116064
ProtChemSI: a network of protein-chemical structural interactions. PMID:22110041
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. PMID:22110027
Predictive models for anti-tubercular molecules using machine learning on high-throughput biological screening datasets. PMID:22099929
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
SuperTarget goes quantitative: update on drug-target interactions. PMID:22067455
SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents. PMID:22067445
Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile. PMID:21980516
Bioinformatics and systems biology of the lipidome. PMID:21939287
PubChem3D: a new resource for scientists. PMID:21933373
Identification of novel functional inhibitors of acid sphingomyelinase. PMID:21909365
In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes. PMID:21877154
Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining. PMID:21834535
Structural diversity of biologically interesting datasets: a scaffold analysis approach. PMID:21824432
Improved genome annotation through untargeted detection of pathway-specific metabolites. PMID:21810208
PubChem3D: Biologically relevant 3-D similarity. PMID:21781288
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles. PMID:21774809
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
A web server for predicting inhibitors against bacterial target GlmU protein. PMID:21733180
Tyrosine kinase syk non-enzymatic inhibitors and potential anti-allergic drug-like compounds discovered by virtual and in vitro screening. PMID:21701581
GPU accelerated chemical similarity calculation for compound library comparison. PMID:21692447
Exploiting PubChem for Virtual Screening. PMID:21691435
Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. PMID:21618009
Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem. PMID:21618008
hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds. PMID:21586548
Combinations of protein-chemical complex structures reveal new targets for established drugs. PMID:21573205
Extending biochemical databases by metabolomic surveys. PMID:21566124
PubChem3D: Similar conformers. PMID:21554721
PubChem3D: Diversity of shape. PMID:21418625
Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. PMID:21417267
Functional characterization of novel mutations in UL54 of ganciclovir resistant HCMV strain using structural analysis. PMID:21383907
Analysis of multiple compound-protein interactions reveals novel bioactive molecules. PMID:21364574
Advances in structure elucidation of small molecules using mass spectrometry. PMID:21289855
PubChem3D: Conformer generation. PMID:21272340
A Java API for working with PubChem datasets. PMID:21216779
Predicting cytotoxicity from heterogeneous data sources with Bayesian learning. PMID:21143909
Database resources of the National Center for Biotechnology Information. PMID:21097890
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. PMID:21087994
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. PMID:21059682
The Text-mining based PubChem Bioassay neighboring analysis. PMID:21059237
PubChem as a public resource for drug discovery. PMID:20970519
SuperSweet--a resource on natural and artificial sweetening agents. PMID:20952410
Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules. PMID:20947527
metaP-server: a web-based metabolomics data analysis tool. PMID:20936179
The Comparative Toxicogenomics Database: update 2011. PMID:20864448
Cheminformatics-based drug design approach for identification of inhibitors targeting the characteristic residues of MMP-13 hemopexin domain. PMID:20824169
Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PMID:20808948
Hashing algorithms and data structures for rapid searches of fingerprint vectors. PMID:20681581
Publishing Chinese medicine knowledge as Linked Data on the Web. PMID:20663193
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. PMID:20650010
Knowledge-based annotation of small molecule binding sites in proteins. PMID:20594344
When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values. PMID:20540577
Molecular modeling of lanthionine synthetase component C-like protein 2: a potential target for the discovery of novel type 2 diabetes prophylactics and therapeutics. PMID:20512604
Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase. PMID:20512516
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. PMID:20478034
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. PMID:20460463
Predicting environmental chemical factors associated with disease-related gene expression data. PMID:20459635
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
iPHACE: integrative navigation in pharmacological space. PMID:20156991
Virtual screening of bioassay data. PMID:20150999
An overview of the PubChem BioAssay resource. PMID:19933261
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome. PMID:19923229
Database resources of the National Center for Biotechnology Information. PMID:19910364
T3DB: a comprehensively annotated database of common toxins and their targets. PMID:19897546
Chemical Entities of Biological Interest: an update. PMID:19854951
The NCBI BioSystems database. PMID:19854944
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:19850718
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. PMID:19843613
A novel method for mining highly imbalanced high-throughput screening data in PubChem. PMID:19825798
Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling. PMID:19825513
The University of Minnesota Biocatalysis/Biodegradation Database: improving public access. PMID:19767608
Physical binding pocket induction for affinity prediction. PMID:19754201
Database resources of the National Center for Biotechnology Information PubMed citations: 375.

375 articles citing: Database resources of the National Center for Biotechnology Information

Enhancing the Discovery of Functional Post-Translational Modification Sites with Machine Learning Models - Development, Validation, and Interpretation. PMID:35696084
The Readthrough Isoform AQP4ex Is Constitutively Phosphorylated in the Perivascular Astrocyte Endfeet of Human Brain. PMID:35625560
The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins. PMID:35610211
VHL-P138R and VHL-L163R Novel Variants: Mechanisms of VHL Pathogenicity Involving HIF-Dependent and HIF-Independent Actions. PMID:35388293
Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. PMID:35351103
Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata. PMID:35309135
A Comprehensive Analysis of Fibrillar Collagens in Lamprey Suggests a Conserved Role in Vertebrate Musculoskeletal Evolution. PMID:35242758
Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science. PMID:35052043
The first comprehensive database of germline pathogenic variants in East Asian cancer patients. PMID:34964846
Unraveling Protein Interactions between the Temperate Virus Bam35 and Its Bacillus Host Using an Integrative Yeast Two Hybrid-High Throughput Sequencing Approach. PMID:34681765
Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling. PMID:34597600
High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases. PMID:34586890
De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. PMID:34532854
Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved. PMID:34193932
LeishIF4E-5 Is a Promastigote-Specific Cap-Binding Protein in Leishmania. PMID:33921489
Is PF-00835231 a Pan-SARS-CoV-2 Mpro Inhibitor? A Comparative Study. PMID:33802860
HARVESTMAN: a framework for hierarchical feature learning and selection from whole genome sequencing data. PMID:33794760
High Quality Aspergillus aculeatus Genomes and Transcriptomes: A Platform for Cellulase Activity Optimization Toward Industrial Applications. PMID:33585410
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Models of the Gene Must Inform Data-Mining Strategies in Genomics. PMID:33286713
A novel Oct4/Pou5f1-like non-coding RNA controls neural maturation and mediates developmental effects of ethanol. PMID:33221301
Cultivable marine fungi from the Arctic Archipelago of Svalbard and their antibacterial activity. PMID:33062384
KGHC: a knowledge graph for hepatocellular carcinoma. PMID:32646496
Identification of Sphingosine Kinase-1 Inhibitors from Bioactive Natural Products Targeting Cancer Therapy. PMID:32596609
Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. PMID:32445281
Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: possible implication in COVID-19 therapy. PMID:32441299
Codon Pairs are Phylogenetically Conserved: A comprehensive analysis of codon pairing conservation across the Tree of Life. PMID:32401752
Chapter 26 The Molecular Libraries Screening Center Network (MLSCN): Identifying Chemical Probes of Biological Systems. PMID:32287469
Virtual Screening Approach to Identify High-Affinity Inhibitors of Serum and Glucocorticoid-Regulated Kinase 1 among Bioactive Natural Products: Combined Molecular Docking and Simulation Studies. PMID:32070031
Lipid Related Genes Altered in NASH Connect Inflammation in Liver Pathogenesis Progression to HCC: A Canonical Pathway. PMID:31717414
Co-expression of synaptic genes in the sponge Amphimedon queenslandica uncovers ancient neural submodules. PMID:31673079
Molecular evolution of the meiotic recombination pathway in mammals. PMID:31579931
High-coverage genomes to elucidate the evolution of penguins. PMID:31531675
CAM: an alignment-free method to recover phylogenies using codon aversion motifs. PMID:31198636
CANCROX: a cross-species cancer therapy database. PMID:31032838
Genetic Variations and Precision Medicine. PMID:31019429
Association of Rare Coding Mutations With Alzheimer Disease and Other Dementias Among Adults of European Ancestry. PMID:30924900
Conserved Disease Modules Extracted From Multilayer Heterogeneous Disease and Gene Networks for Understanding Disease Mechanisms and Predicting Disease Treatments. PMID:30713550
A study in scarlet: MC1R as the main predictor of red hair and exemplar of the flip-flop effect. PMID:30657907
ExtRamp: a novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness. PMID:30649455
Miniscule differences between sex chromosomes in the giant genome of a salamander. PMID:30552368
Lack of UGT polymorphism association with idasanutlin pharmacokinetics in solid tumor patients. PMID:30511219
Thirty biologically interpretable clusters of transcription factors distinguish cancer type. PMID:30305013
Universal method for robust detection of circadian state from gene expression. PMID:30201705
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. PMID:30120140
Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms. PMID:30042519
A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae. PMID:29873704
Inferring duplication episodes from unrooted gene trees. PMID:29745844
Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss. PMID:29608732
Characterization of indole-3-pyruvic acid pathway-mediated biosynthesis of auxin in Neurospora crassa. PMID:29420579
Preferential selection of Arginine at the lipid-water-interface of TRPV1 during vertebrate evolution correlates with its snorkeling behaviour and cholesterol interaction. PMID:29196683
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data. PMID:29019934
Identification of a novel variant of the RET proto-oncogene in a novel family with Hirschsprung's disease. PMID:28799054
Biodeterioration of Pompeian mural paintings: fungal colonization favoured by the presence of volcanic material residues. PMID:28681298
Replications of Two Closely Related Groups of Jumbo Phages Show Different Level of Dependence on Host-encoded RNA Polymerase. PMID:28659872
Genome sequence variation in the constricta strain dramatically alters the protein interaction and localization map of Potato yellow dwarf virus. PMID:28635588
The most common technologies and tools for functional genome analysis. PMID:28630587
Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage. PMID:28542527
An ontology-based search engine for digital reconstructions of neuronal morphology. PMID:28337675
Understanding the conservation patterns and molecular phylogenetics of human death receptors family through computational biology. PMID:28324447
Insights into the molecular mechanisms of Polygonum multiflorum Thunb-induced liver injury: a computational systems toxicology approach. PMID:28239160
Phylogenetic Tree Analysis of the Cold-Hot Nature of Traditional Chinese Marine Medicine for Possible Anticancer Activity. PMID:28191021
Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation. PMID:28118853
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. PMID:28092920
Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni. PMID:28050056
Intragenic Deletions in ATP7B as an Unusual Molecular Genetics Mechanism of Wilson's Disease Pathogenesis. PMID:27992490
Comparative transcriptional profile of the fish parasite Cryptocaryon irritans. PMID:27923398
Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. PMID:27716510
Digital PCR Panel for Sensitive Hematopoietic Chimerism Quantification after Allogeneic Stem Cell Transplantation. PMID:27618030
Single-sample expression-based chemo-sensitivity score improves survival associations independently from genomic mutations for ovarian cancer Patients. PMID:27570657
Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. PMID:27489570
Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PMID:27467773
Effects of Lead and Mercury on Sulfate-Reducing Bacterial Activity in a Biological Process for Flue Gas Desulfurization Wastewater Treatment. PMID:27455890
Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract. PMID:27445992
Molecular Characterisation and Co-cultivation of Bacterial Biofilm Communities Associated with the Mat-Forming Diatom Didymosphenia geminata. PMID:27412380
RNAlien - Unsupervised RNA family model construction. PMID:27330139
Genomic Analysis Unravels Reduced Inorganic Sulfur Compound Oxidation of Heterotrophic Acidophilic Acidicaldus sp. Strain DX-1. PMID:27239474
Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses. PMID:27190508
Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification. PMID:27175227
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination. PMID:27031986
Why individual thermo sensation and pain perception varies? Clue of disruptive mutations in TRPVs from 2504 human genome data. PMID:26962677
Metabolomics in rheumatic diseases: desperately seeking biomarkers. PMID:26935283
A novel HCFC1 variant in male siblings with intellectual disability and microcephaly in the absence of cobalamin disorder. PMID:26893841
Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. PMID:26830287
Estimation of Inhibitory Effect against Tyrosinase Activity through Homology Modeling and Molecular Docking. PMID:26788364
A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays. PMID:26764274
UCSC Data Integrator and Variant Annotation Integrator. PMID:26740527
Genetic associations and shared environmental effects on the skin microbiome of Korean twins. PMID:26596276
Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution. PMID:26500819
Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel). PMID:26442818
Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test. PMID:26369336
Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples. PMID:26318339
Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria. PMID:26074885
An Ebola virus-centered knowledge base. PMID:26055098
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. PMID:26052341
Antennal Transcriptome Analysis of Odorant Reception Genes in the Red Turpentine Beetle (RTB), Dendroctonus valens. PMID:25938508
Antitumor Activities of Ethyl Acetate Extracts from Selaginella doederleinii Hieron In Vitro and In Vivo and Its Possible Mechanism. PMID:25866543
Meta-Analysis of Gene Expression in Autism Spectrum Disorder. PMID:25720351
Co-occurrence of four nucleotide changes associated with an adult mitochondrial ataxia phenotype. PMID:25488682
Text mining in cancer gene and pathway prioritization. PMID:25392685
Semi-automated literature mining to identify putative biomarkers of disease from multiple biofluids. PMID:25379168
DEOP: a database on osmoprotectants and associated pathways. PMID:25326239
RADB: a database of rheumatoid arthritis-related polymorphisms. PMID:25228593
Big data in chemical toxicity research: the use of high-throughput screening assays to identify potential toxicants. PMID:25195622
A novel mutation in the transglutaminase-1 gene in an autosomal recessive congenital ichthyosis patient. PMID:25180191
Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase. PMID:25165734
Network based integrated analysis of phenotype-genotype data for prioritization of candidate symptom genes. PMID:24991551
Integrative analysis of independent transcriptome data for rare diseases. PMID:24981076
Insilico docking study of compounds elucidated from helicteres isora fruits with ampkinase- insulin receptor. PMID:24966532
Metabolic characteristics of a glycogen-accumulating organism in Defluviicoccus cluster II revealed by comparative genomics. PMID:24889288
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). PMID:24742296
NatalieQ: a web server for protein-protein interaction network querying. PMID:24690407
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
Angiotensin II-induced cardiovascular load regulates cardiac remodeling and related gene expression in late-gestation fetal sheep. PMID:24614802
Do photobiont switch and cephalodia emancipation act as evolutionary drivers in the lichen symbiosis? A case study in the Pannariaceae (Peltigerales). PMID:24587091
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. PMID:24571547
Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium. PMID:24568933
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. PMID:24441647
Identification and characterization of seven glutathione S-transferase genes from citrus red mite, Panonychus citri (McGregor). PMID:24351815
A metagenomic framework for the study of airborne microbial communities. PMID:24349140
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PMID:24340000
Enhancing systems medicine beyond genotype data by dynamic patient signatures: having information and using it too. PMID:24312119
Identification of putative ortholog gene blocks involved in gestant and lactating mammary gland development: a rodent cross-species microarray transcriptomics approach. PMID:24288657
Anolis sex chromosomes are derived from a single ancestral pair. PMID:24279795
Differences in the structure of the gut bacteria communities in development stages of the Chinese white pine beetle (Dendroctonus armandi). PMID:24145750
Characterization of bacteriophages Cp1 and Cp2, the strain-typing agents for Xanthomonas axonopodis pv. citri. PMID:24123743
Combining genetic association study designs: a GWAS case study. PMID:24098305
Evaluation of genome sequencing quality in selected plant species using expressed sequence tags. PMID:23922843
Unraveling genomic variation from next generation sequencing data. PMID:23885890
Drug repositioning: a machine-learning approach through data integration. PMID:23800010
Finding potentially new multimorbidity patterns of psychiatric and somatic diseases: exploring the use of literature-based discovery in primary care research. PMID:23775174
The evolutionary portrait of metazoan NAD salvage. PMID:23724078
QA-RecombineIt: a server for quality assessment and recombination of protein models. PMID:23700309
Developmental gene discovery in a hemimetabolous insect: de novo assembly and annotation of a transcriptome for the cricket Gryllus bimaculatus. PMID:23671567
Genome-wide analysis of immune system genes by expressed sequence Tag profiling. PMID:23616578
Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes. PMID:23606477
TUMIR: an experimentally supported database of microRNA deregulation in various cancers. PMID:23594715
DNA variations in oculocutaneous albinism: an updated mutation list and current outstanding issues in molecular diagnostics. PMID:23504663
PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress. PMID:23448274
Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain. PMID:23440889
SPA: a short peptide assembler for metagenomic data. PMID:23435317
Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFβ3-knockout mice alleles: RNA-Seq analysis of TGFβ3 Mice. PMID:23421592
The transcriptional and gene regulatory network of Lactococcus lactis MG1363 during growth in milk. PMID:23349698
Phylogeny of Toll-like receptor signaling: adapting the innate response. PMID:23326591
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset. PMID:23282181
Insights from the predicted interactions of plant derived compounds to the gluco-corticoid receptor as an alternative to dexa-methasone. PMID:23275688
FlyBase: improvements to the bibliography. PMID:23125371
The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential. PMID:23083487
Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis. PMID:23046677
Separating metagenomic short reads into genomes via clustering. PMID:23009059
Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions. PMID:22963132
Genome-wide association study of obsessive-compulsive disorder. PMID:22889921
A three-dimensional topology of complex I inferred from evolutionary correlations. PMID:22857522
Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. PMID:22848105
Chromatin organization is a major influence on regional mutation rates in human cancer cells. PMID:22820252
BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. PMID:22675348
Genovar: a detection and visualization tool for genomic variants. PMID:22594998
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. PMID:22563243
Conservation of tubulin-binding sequences in TRPV1 throughout evolution. PMID:22496727
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
An examination of the OMIM database for associating mutation to a consensus reference sequence. PMID:22477700
A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses. PMID:22417913
Novel NaPi-IIc mutations causing HHRH and idiopathic hypercalciuria in several unrelated families: long-term follow-up in one kindred. PMID:22387237
Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. PMID:22319178
S279 point mutations in Candida albicans Sterol 14-α demethylase (CYP51) reduce in vitro inhibition by fluconazole. PMID:22252802
Partition decoupling for multi-gene analysis of gene expression profiling data. PMID:22208906
Concentration dependent ion selectivity in VDAC: a molecular dynamics simulation study. PMID:22164223
Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome. PMID:22128332
A unified framework for managing provenance information in translational research. PMID:22126369
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach. PMID:21912686
Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration. PMID:21863139
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network. PMID:21818306
Successful COG8 and PDF overlap is mediated by alterations in splicing and polyadenylation signals. PMID:21805148
Characterisation of a desmosterol reductase involved in phytosterol dealkylation in the silkworm, Bombyx mori. PMID:21738635
Molecular modelling of the emergence of azole resistance in Mycosphaerella graminicola. PMID:21738598
New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PMID:21720552
Positional orthology: putting genomic evolutionary relationships into context. PMID:21705766
Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. PMID:21700957
Sporisorium reilianum infection changes inflorescence and branching architectures of maize. PMID:21653782
OrthoList: a compendium of C. elegans genes with human orthologs. PMID:21647448
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. PMID:21595981
Extending biochemical databases by metabolomic surveys. PMID:21566124
Gains, losses and changes of function after gene duplication: study of the metallothionein family. PMID:21541013
An evolutionary genomic approach to identify genes involved in human birth timing. PMID:21533219
Impact of recently emerged sterol 14{alpha}-demethylase (CYP51) variants of Mycosphaerella graminicola on azole fungicide sensitivity. PMID:21478305
Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. PMID:21417267
Vertebrate paralogous MEF2 genes: origin, conservation, and evolution. PMID:21394201
Exploring the evolutionary relationship of insulin receptor substrate family using computational biology. PMID:21364910
The human serum metabolome. PMID:21359215
Quantitative metagenomic analyses based on average genome size normalization. PMID:21317268
Structural assessment of the effects of amino acid substitutions on protein stability and protein protein interaction. PMID:21297231
Analysis of human APOBEC3H haplotypes and anti-human immunodeficiency virus type 1 activity. PMID:21270145
MicroRNAs: Meta-controllers of gene expression in synaptic activity emerge as genetic and diagnostic markers of human disease. PMID:21256154
STITCH: algorithm to splice, trim, identify, track, and capture the uniqueness of 16S rRNAs sequence pairs using public or in-house database. PMID:21113709
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage. PMID:21062824
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. PMID:21044364
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. PMID:20937630
ChemProt: a disease chemical biology database. PMID:20935044
The BioPAX community standard for pathway data sharing. PMID:20829833
Transcript analysis of stem cells. PMID:20816160
Pathophysiological mechanisms of dominant and recessive GLRA1 mutations in hyperekplexia. PMID:20631190
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. PMID:20613790
Orthology confers intron position conservation. PMID:20598118
Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. PMID:20576738
Reconstructing disease outbreaks from genetic data: a graph approach. PMID:20551981
When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values. PMID:20540577
Frog2: Efficient 3D conformation ensemble generator for small compounds. PMID:20444874
Systems biology in heart diseases. PMID:20411053
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. PMID:20122211
A side effect resource to capture phenotypic effects of drugs. PMID:20087340
BLAST-EXPLORER helps you building datasets for phylogenetic analysis. PMID:20067610
A protocol for generating a high-quality genome-scale metabolic reconstruction. PMID:20057383
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. PMID:20053291
Integrative approaches to the prediction of protein functions based on the feature selection. PMID:20043848
Modal codon usage: assessing the typical codon usage of a genome. PMID:20018979
Archiving next generation sequencing data. PMID:19965774
Sp2 is a maternally inherited transcription factor required for embryonic development. PMID:19959469
Integrative predictive model of coronary artery calcification in atherosclerosis. PMID:19948975
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. PMID:19943962
Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication. PMID:19930686
Dynamism in gene expression across multiple studies. PMID:19920211
STITCH 2: an interaction network database for small molecules and proteins. PMID:19897548
Adenosine deamination in human transcripts generates novel microRNA binding sites. PMID:19776031
Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii. PMID:19717546
Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'. PMID:19622150
Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. PMID:19609266
The Chicken Gene Nomenclature Committee report. PMID:19607656
Automated database mediation using ontological metadata mappings. PMID:19567801
Definition, conservation and epigenetics of housekeeping and tissue-enriched genes. PMID:19534766
EDGAR: a software framework for the comparative analysis of prokaryotic genomes. PMID:19457249
Checklist for optimization and validation of real-time PCR assays. PMID:19455629
Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment. PMID:19426482
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists. PMID:19420064
SysPTM: a systematic resource for proteomic research on post-translational modifications. PMID:19366988
Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii. PMID:19359364
TFCat: the curated catalog of mouse and human transcription factors. PMID:19284633
Reconstruction of metabolic pathways for the cattle genome. PMID:19284618
A census of human transcription factors: function, expression and evolution. PMID:19274049
Prediction of interaction between small molecule and enzyme using AdaBoost. PMID:19219560
MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data. PMID:19208617
Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology. PMID:19208187
Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays. PMID:19208186
Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom. PMID:19192293
Phylogenetic and functional assessment of orthologs inference projects and methods. PMID:19148271
Detailed transcriptome atlas of the pancreatic beta cell. PMID:19146692
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. PMID:19136627
Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system. PMID:19126580
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network. PMID:19094223
Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry. PMID:19091013
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. PMID:19091010
Functional analysis of novel SNPs and mutations in human and mouse genomes. PMID:19091009
A snapshot of CNVs in the pig genome. PMID:19079605
Data mining of cancer vaccine trials: a bird's-eye view. PMID:19077266
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. PMID:19074493
Genotype-phenotype databases: challenges and solutions for the post-genomic era. PMID:19065136
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics. PMID:19055845
Algorithm of OMA for large-scale orthology inference. PMID:19055798
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. PMID:19036792
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
BloodExpress: a database of gene expression in mouse haematopoiesis. PMID:18987008
Bionemo: molecular information on biodegradation metabolism. PMID:18986994
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. PMID:18978025
In silico identification of specialized secretory-organelle proteins in apicomplexan parasites and in vivo validation in Toxoplasma gondii. PMID:18974850
Defrosting the digital library: bibliographic tools for the next generation web. PMID:18974831
Implementation of GenePattern within the Stanford Microarray Database. PMID:18953035
ATTED-II provides coexpressed gene networks for Arabidopsis. PMID:18953027
HMDB: a knowledgebase for the human metabolome. PMID:18953024
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. PMID:18927222
miR2Disease: a manually curated database for microRNA deregulation in human disease. PMID:18927107
Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease. PMID:18853455
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. PMID:18846089
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. PMID:18842600
XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data. PMID:18840282
Interspecies data mining to predict novel ING-protein interactions in human. PMID:18801192
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. PMID:18752676
Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. PMID:18728074
Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence. PMID:18705888
Variations in the ghrelin receptor gene associate with obesity and glucose metabolism in individuals with impaired glucose tolerance. PMID:18698404
Computational analysis of the human HSPH/HSPA/DNAJ family and cloning of a human HSPH/HSPA/DNAJ expression library. PMID:18686016
Genes to diseases (G2D) computational method to identify asthma candidate genes. PMID:18682798
Phylogenetic analyses suggest multiple changes of substrate specificity within the glycosyl hydrolase 20 family. PMID:18647384
Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy. PMID:18636118
An insect virus-encoded microRNA regulates viral replication. PMID:18614632
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. PMID:18613946
A maximum common substructure-based algorithm for searching and predicting drug-like compounds. PMID:18586736
The effectiveness of position- and composition-specific gap costs for protein similarity searches. PMID:18586708
Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. PMID:18577208
PURE: a webserver for the prediction of domains in unassigned regions in proteins. PMID:18554415
Anni 2.0: a multipurpose text-mining tool for the life sciences. PMID:18549479
Predicting failure rate of PCR in large genomes. PMID:18492719
Automated comparative auditing of NCIT genomic roles using NCBI. PMID:18486558
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. PMID:18460543
Designating eukaryotic orthology via processed transcription units. PMID:18445630
GenoWatch: a disease gene mining browser for association study. PMID:18440974
Identification of outer membrane proteins of Mycobacterium tuberculosis. PMID:18439872
Regulation of glycan structures in animal tissues: transcript profiling of glycan-related genes. PMID:18411279
ReXSpecies--a tool for the analysis of the evolution of gene regulation across species. PMID:18410675
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. PMID:18402669
Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective. PMID:18397526
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. PMID:18371204
A virtual computer lab for distance biomedical technology education. PMID:18366629
Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts. PMID:18325113
Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. PMID:18315849
New classification of HLA-DRB1 alleles in rheumatoid arthritis susceptibility: a combined analysis of worldwide samples. PMID:18307784
Gene conversion in the rice genome. PMID:18298833
Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. PMID:18296538
Homology and phylogeny and their automated inference. PMID:18288471
Phylogenetic classification of short environmental DNA fragments. PMID:18285365
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. PMID:18279518
The genome landscape of ERalpha- and ERbeta-binding DNA regions. PMID:18272478
Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PMID:18270584
Bioinformatics and cancer research: building bridges for translational research. PMID:18258507
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. PMID:18254954
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Universal seeds for cDNA-to-genome comparison. PMID:18215286
The UCSC Genome Browser Database: 2008 update. PMID:18086701
STITCH: interaction networks of chemicals and proteins. PMID:18084021
Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies. PMID:18065537
Amyotrophic lateral sclerosis: an emerging era of collaborative gene discovery. PMID:18060051
Towards completion of the Earth's proteome. PMID:18059312
The genome browser at UCSC for locating genes, and much more! PMID:18058261
TreeFam: 2008 Update. PMID:18056084
InParanoid 6: eukaryotic ortholog clusters with inparalogs. PMID:18055500
DrugBank: a knowledgebase for drugs, drug actions and drug targets. PMID:18048412
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. PMID:18042280
CandidaDB: a multi-genome database for Candida species and related Saccharomycotina. PMID:18039716
The Pfam protein families database. PMID:18039703
Microarray expression profiles of 20.000 genes across 23 healthy porcine tissues. PMID:18030337
e-Fungi: a data resource for comparative analysis of fungal genomes. PMID:18028535
The Molecular Biology Database Collection: 2008 update. PMID:18025043
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. PMID:18021451
Ensembl 2008. PMID:18000006
NONCODE v2.0: decoding the non-coding. PMID:18000000
Update of ASRP: the Arabidopsis Small RNA Project database. PMID:17999994
A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. PMID:17999775
The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. PMID:17996046
MEROPS: the peptidase database. PMID:17991683
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update. PMID:17986454
The HGNC Database in 2008: a resource for the human genome. PMID:17984084
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. PMID:17984082
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. PMID:17984073
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. PMID:17982176
Narcisse: a mirror view of conserved syntenies. PMID:17981845
The Molecule Pages database. PMID:17965093
Exonization of active mouse L1s: a driver of transcriptome evolution? PMID:17963496
Human PAML browser: a database of positive selection on human genes using phylogenetic methods. PMID:17962310
MetaLook: a 3D visualisation software for marine ecological genomics. PMID:17953757
ChemBank: a small-molecule screening and cheminformatics resource database. PMID:17947324
Gallus GBrowse: a unified genomic database for the chicken. PMID:17933775
ATDB: a uni-database platform for animal toxins. PMID:17933766
Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system. PMID:17933763
MUGEN mouse database; animal models of human immunological diseases. PMID:17932065
COXPRESdb: a database of coexpressed gene networks in mammals. PMID:17932064
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
NORINE: a database of nonribosomal peptides. PMID:17913739
SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. PMID:17884916
Integrating sequence and structural biology with DAS. PMID:17850653
Structural characteristics of zebrafish orthologs of adaptor molecules that associate with transmembrane immune receptors. PMID:17719728
In Silico characterization of phosphorylase kinase: evidence for an alternate intronic polyadenylation site in PHKG1. PMID:17692548
PepBank--a database of peptides based on sequence text mining and public peptide data sources. PMID:17678535
Conducting research on the web: 2007 update for the bioinformatics links directory. PMID:17586821
Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization. PMID:17584922
Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells. PMID:17553482
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. PMID:17488840
Frog: a FRee Online druG 3D conformation generator. PMID:17485475
iHOP web services. PMID:17485473
CARGO: a web portal to integrate customized biological information. PMID:17483515
Update of the G2D tool for prioritization of gene candidates to inherited diseases. PMID:17478516
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. PMID:17452348
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. PMID:17343765
PubChem's BioAssay Database PubMed citations: 169.

169 articles citing: PubChem's BioAssay Database

Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. PMID:35819579
Pharmacological analysis of Empagliflozin: Acting through the CaMKII pathway in type 2 diabetes and acute cardiovascular events. PMID:35767566
Network pharmacological analysis of active components of Tongqiao Huoxue Decoction in the treatment of intracerebral hemorrhage. PMID:35722393
Protective Effects and Mechanisms of Yinchen Linggui Zhugan Decoction in HFD-Induced Nonalcoholic Fatty Liver Disease Rats Based on Network Pharmacology and Experimental Verification. PMID:35721171
Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase. PMID:35625201
The potential effects and mechanisms of hispidulin in the treatment of diabetic retinopathy based on network pharmacology. PMID:35590353
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. PMID:35579568
Predicting circRNA-drug sensitivity associations via graph attention auto-encoder. PMID:35508967
Screening and Validation of a Carvacrol-Targeting Viability-Regulating Protein, SLC6A3, in Liver Hepatocellular Carcinoma. PMID:35401884
Pocket2Drug: An Encoder-Decoder Deep Neural Network for the Target-Based Drug Design. PMID:35359869
A novel signature based on autophagy-related lncRNA for prognostic prediction and candidate drugs for lung adenocarcinoma. PMID:35261881
MolData, a molecular benchmark for disease and target based machine learning. PMID:35255958
Plasma lipidomics analysis reveals altered lipids signature in patients with osteonecrosis of the femoral head. PMID:35147763
Developments in high-resolution mass spectrometric analyses of new psychoactive substances. PMID:35141767
Network Pharmacology and Experimental Assessment to Explore the Pharmacological Mechanism of Qimai Feiluoping Decoction Against Pulmonary Fibrosis. PMID:34925028
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning. PMID:34600569
Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks. PMID:34590285
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
Newly designed compounds from scaffolds of known actives as inhibitors of survivin: computational analysis from the perspective of fragment-based drug design. PMID:34350094
NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. PMID:34340747
The Potential Effect of Rhizoma coptidis on Polycystic Ovary Syndrome Based on Network Pharmacology and Molecular Docking. PMID:34306142
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Elucidating direct kinase targets of compound Danshen dropping pills employing archived data and prediction models. PMID:33953309
Bioactivity Signatures of Drugs vs. Environmental Chemicals Revealed by Tox21 High-Throughput Screening Assays. PMID:33693373
Oleate-induced aggregation of LC3 at the trans-Golgi network is linked to a protein trafficking blockade. PMID:33335289
Compounds with Antiviral, Anti-Inflammatory and Anticancer Activity Identified in Wine from Hungary's Tokaj Region via High Resolution Mass Spectrometry and Bioinformatics Analyses. PMID:33334025
Repurposing therapeutics for COVID-19: Rapid prediction of commercially available drugs through machine learning and docking. PMID:33180803
Biological network analysis with deep learning. PMID:33169146
Changing the HTS Paradigm: AI-Driven Iterative Screening for Hit Finding. PMID:32808550
HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs. PMID:32746900
Computational Chemogenomics Drug Repositioning Strategy Enables the Discovery of Epirubicin as a New Repurposed Hit for Plasmodium falciparum and P. vivax. PMID:32601162
Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement. PMID:32575564
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease. PMID:32530282
Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells. PMID:32325755
Deep Learning-driven research for drug discovery: Tackling Malaria. PMID:32069285
Integrative Multi-Kinase Approach for the Identification of Potent Antiplasmodial Hits. PMID:31824917
Targeting HIV/HCV Coinfection Using a Machine Learning-Based Multiple Quantitative Structure-Activity Relationships (Multiple QSAR) Method. PMID:31336592
Structural and Functional Characterization of PR-4 SUGARWINs From Sugarcaneand Their Role in Plant Defense. PMID:30666261
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
Molecular insight to size and dose-dependent cellular toxicity exhibited by a green synthesized bioceramic nanohybrid with macrophages for dental applications. PMID:30310673
Exploring a new ligand binding site of G protein-coupled receptors. PMID:30310578
Behavioral Effects of a Potential Novel TAAR1 Antagonist. PMID:30233365
Dark chemical matter in public screening assays and derivation of target hypotheses. PMID:30108727
Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data. PMID:30090397
Exploring Structural Relationships between Bioactive and Commercial Chemical Space and Developing Target Hypotheses for Compound Acquisition. PMID:30023563
Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds. PMID:29990427
Naïve Bayesian Models for Vero Cell Cytotoxicity. PMID:29959603
High-Throughput Screening Assay Datasets from the PubChem Database. PMID:29795804
MoleculeNet: a benchmark for molecular machine learning. PMID:29629118
Series of screening compounds with high hit rates for the exploration of multi-target activities and assay interference. PMID:29568568
An automated framework for QSAR model building. PMID:29340790
The CompTox Chemistry Dashboard: a community data resource for environmental chemistry. PMID:29185060
Evidence-Based Precision Oncology with the Cancer Targetome. PMID:28964549
Informatics Approaches for Predicting, Understanding, and Testing Cancer Drug Combinations. PMID:28730498
Entering the 'big data' era in medicinal chemistry: molecular promiscuity analysis revisited. PMID:28670471
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. PMID:28577120
Harnessing plant metabolic diversity. PMID:28527344
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. PMID:28444480
PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing. PMID:28346087
Structure-Promiscuity Relationship Puzzles-Extensively Assayed Analogs with Large Differences in Target Annotations. PMID:28265982
Large-scale bioactivity analysis of the small-molecule assayed proteome. PMID:28178331
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. PMID:28007024
PubChem BioAssay: 2017 update. PMID:27899599
The Principles of Ligand Specificity on beta-2-adrenergic receptor. PMID:27703221
Molecular graph convolutions: moving beyond fingerprints. PMID:27558503
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets. PMID:27515740
Virtual Screening of DrugBank Reveals Two Drugs as New BCRP Inhibitors. PMID:27401583
Comparison of Points of Departure for Health Risk Assessment Based on High-Throughput Screening Data. PMID:27384688
bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. PMID:27367556
CART-a chemical annotation retrieval toolkit. PMID:27256313
Determining the Degree of Promiscuity of Extensively Assayed Compounds. PMID:27082988
In silico methods for drug repurposing and pharmacology. PMID:27080087
Modern approaches to accelerate discovery of new antischistosomal drugs. PMID:27073973
Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders. PMID:27073698
Predicting drug target interactions using meta-path-based semantic network analysis. PMID:27071755
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Chemoinformatics: Achievements and Challenges, a Personal View. PMID:26828468
Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases. PMID:26703541
Mining Chemical Activity Status from High-Throughput Screening Assays. PMID:26658480
Database resources of the National Center for Biotechnology Information. PMID:26615191
Target enhanced 2D similarity search by using explicit biological activity annotations and profiles. PMID:26583046
WITHDRAWN--a resource for withdrawn and discontinued drugs. PMID:26553801
Can Invalid Bioactives Undermine Natural Product-Based Drug Discovery? PMID:26505758
Dark chemical matter as a promising starting point for drug lead discovery. PMID:26479441
In silico exploration of c-KIT inhibitors by pharmaco-informatics methodology: pharmacophore modeling, 3D QSAR, docking studies, and virtual screening. PMID:26416560
Predicting Mouse Liver Microsomal Stability with "Pruned" Machine Learning Models and Public Data. PMID:26415647
PubChem Substance and Compound databases. PMID:26400175
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. PMID:26322135
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
PubChem atom environments. PMID:26300985
Prediction of human population responses to toxic compounds by a collaborative competition. PMID:26258538
PhIN: A Protein Pharmacology Interaction Network Database. PMID:26225242
Activity, assay and target data curation and quality in the ChEMBL database. PMID:26201396
Reporting biological assay screening results for maximum impact. PMID:26194585
Fluorometric CCHFV OTU protease assay with potent inhibitors. PMID:26156848
PubChem structure-activity relationship (SAR) clusters. PMID:26150895
Promiscuity progression of bioactive compounds over time. PMID:26064479
Cheminformatics models based on machine learning approaches for design of USP1/UAF1 abrogators as anticancer agents. PMID:25972987
ChEMBL web services: streamlining access to drug discovery data and utilities. PMID:25883136
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
QSAR-assisted virtual screening of lead-like molecules from marine and microbial natural sources for antitumor and antibiotic drug discovery. PMID:25789820
Prediction of drug-ABC-transporter interaction--Recent advances and future challenges. PMID:25769815
When drug discovery meets web search: Learning to Rank for ligand-based virtual screening. PMID:25705262
Global analysis reveals families of chemical motifs enriched for HERG inhibitors. PMID:25700001
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PMID:25670818
A ranking method for the concurrent learning of compounds with various activity profiles. PMID:25643067
In silico repositioning-chemogenomics strategy identifies new drugs with potential activity against multiple life stages of Schistosoma mansoni. PMID:25569258
Benchmarking methods and data sets for ligand enrichment assessment in virtual screening. PMID:25481478
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. PMID:25477388
Assessing HTS performance using BioAssay Ontology: screening and analysis of a bacterial phospho-N-acetylmuramoyl-pentapeptide translocase campaign. PMID:25415593
Database resources of the National Center for Biotechnology Information. PMID:25398906
Effective chemical constituent's identification of extracting solution from herbs - a review. PMID:25371564
Activity artifacts in drug discovery and different facets of compound promiscuity. PMID:25339989
Curation and analysis of multitargeting agents for polypharmacological modeling. PMID:25133604
The influence of negative training set size on machine learning-based virtual screening. PMID:24976867
A controlled vocabulary for pathway entities and events. PMID:24951798
Profiling animal toxicants by automatically mining public bioassay data: a big data approach for computational toxicology. PMID:24950175
Experimental validation of FINDSITE(comb) virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. PMID:24936211
In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. PMID:24928891
Antiproliferative activity of the Michael adducts of aroylacrylic acids and cyclic amines. PMID:24874228
Many approved drugs have bioactive analogs with different target annotations. PMID:24871342
Exploring compound promiscuity patterns and multi-target activity spaces. PMID:24688751
In vitro and in vivo activities of HPi1, a selective antimicrobial against Helicobacter pylori. PMID:24687512
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
Advancing the activity cliff concept. PMID:24555097
A chemoinformatics approach to the discovery of lead-like molecules from marine and microbial sources en route to antitumor and antibiotic drugs. PMID:24473174
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. PMID:24470572
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. PMID:24441647
Cofactor-independent phosphoglycerate mutase from nematodes has limited druggability, as revealed by two high-throughput screens. PMID:24416464
Identification of Small-Molecule Frequent Hitters from AlphaScreen High-Throughput Screens. PMID:24371213
Amyloid-precursor-protein-lowering small molecules for disease modifying therapy of Alzheimer's disease. PMID:24367508
Web search and data mining of natural products and their bioactivities in PubChem. PMID:24363665
An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data. PMID:24331047
Database resources of the National Center for Biotechnology Information. PMID:24259429
FireDB: a compendium of biological and pharmacologically relevant ligands. PMID:24243844
Integrating in silico resources to map a signaling network. PMID:24233784
The ChEMBL bioactivity database: an update. PMID:24214965
PubChem BioAssay: 2014 update. PMID:24198245
DGIdb: mining the druggable genome. PMID:24122041
Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PMID:24068907
A functional siRNA screen identifies genes modulating angiotensin II-mediated EGFR transactivation. PMID:24046455
Aurintricarboxylic acid modulates the affinity of hepatitis C virus NS3 helicase for both nucleic acid and ATP. PMID:23947785
Systematic study of mitochondrial toxicity of environmental chemicals using quantitative high throughput screening. PMID:23895456
Plurigon: three dimensional visualization and classification of high-dimensionality data. PMID:23885241
Predicting the protein targets for athletic performance-enhancing substances. PMID:23800040
A unified proteochemometric model for prediction of inhibition of cytochrome p450 isoforms. PMID:23799117
Contributions of academic laboratories to the discovery and development of chemical biology tools. PMID:23672690
What is the likelihood of an active compound to be promiscuous? Systematic assessment of compound promiscuity on the basis of PubChem confirmatory bioassay data. PMID:23605807
The influence of the inactives subset generation on the performance of machine learning methods. PMID:23561266
Discovering new medicines targeting helicases: challenges and recent progress. PMID:23536547
Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases. PMID:23447100
A detailed physiologically based model to simulate the pharmacokinetics and hormonal pharmacodynamics of enalapril on the circulating endocrine Renin-Angiotensin-aldosterone system. PMID:23404365
Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account. PMID:23296990
Polypharmacology: drug discovery for the future. PMID:23272792
Taking Open Innovation to the Molecular Level - Strengths and Limitations. PMID:23226167
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
Database resources of the National Center for Biotechnology Information. PMID:23193264
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis. PMID:23134593
SwissSidechain: a molecular and structural database of non-natural sidechains. PMID:23104376
The Comparative Toxicogenomics Database: update 2013. PMID:23093600
The effect of curcumin on human bronchial epithelial cells exposed to fine particulate matter: a predictive analysis. PMID:23090021
Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software. PMID:23088273
Inhibitors of Streptococcus pneumoniae surface endonuclease EndA discovered by high-throughput screening using a PicoGreen fluorescence assay. PMID:23015019
Identification and analysis of hepatitis C virus NS3 helicase inhibitors using nucleic acid binding assays. PMID:22740655
Public domain databases for medicinal chemistry. PMID:22731701
Structure based virtual screening of novel inhibitors against multidrug resistant superbugs. PMID:22715312
Behavioral barcoding in the cloud: embracing data-intensive digital phenotyping in neuropharmacology. PMID:22652049
FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. PMID:22574683
PubChem BioAssay: 2017 update PubMed citations: 142.

142 articles citing: PubChem BioAssay: 2017 update

Active ingredients and molecular targets of Taraxacum mongolicum against hepatocellular carcinoma: network pharmacology, molecular docking, and molecular dynamics simulation analysis. PMID:35873910
Comprehensive Bioinformatics Analysis to Reveal Key RNA Targets and Hub Competitive Endogenous RNA Network of Keratoconus. PMID:35747602
Using BERT to identify drug-target interactions from whole PubMed. PMID:35729494
Network pharmacological analysis of active components of Tongqiao Huoxue Decoction in the treatment of intracerebral hemorrhage. PMID:35722393
Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs. PMID:35672835
Drug Design by Pharmacophore and Virtual Screening Approach. PMID:35631472
DeepNC: a framework for drug-target interaction prediction with graph neural networks. PMID:35578674
Computational method for estimating progression saturation of analog series. PMID:35542404
In silico bioprospecting of taraxerol as a main protease inhibitor of SARS-CoV-2 to develop therapy against COVID-19. PMID:35502321
Predicting hERG channel blockers with directed message passing neural networks. PMID:35425351
Prediction of the Active Components and Possible Targets of Xanthii Fructus Based on Network Pharmacology for Use in Chronic Rhinosinusitis. PMID:35287308
[Identification of traditional Chinese drugs containing active ingredients for treating myocardial infarction and analysis of their therapeutic mechanisms by network pharmacology and molecular docking]. PMID:35249866
Network pharmacology analysis and experimental study strategy reveals the potential mechanism of puerarin against rotavirus. PMID:35242859
Sequence-based prediction of protein binding regions and drug-target interactions. PMID:35135622
A Preliminary Inquiry Into the Potential Mechanism of Huang-Lian-Jie-Du Decoction in Treating Rheumatoid Arthritis via Network Pharmacology and Molecular Docking. PMID:35127697
Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9. PMID:35081108
The possible mechanism of Hippophae fructus oil applied in tympanic membrane repair identified based on network pharmacology and molecular docking. PMID:34859918
Effects and Components of Herb Pair Huanglian-Banxia on Diabetic Gastroparesis by Network Pharmacology. PMID:34708128
Point mutations in Candida glabrata 3-hydroxy-3-methylglutaryl-coenzyme A reductase (CgHMGR) decrease enzymatic activity and substrate/inhibitor affinity. PMID:34675283
Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks. PMID:34590285
Comprehensive Survey of Recent Drug Discovery Using Deep Learning. PMID:34576146
Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on "drug-target-pathway" heterogenous network. PMID:34544480
Recent Advances in In Silico Target Fishing. PMID:34500568
De novo molecular drug design benchmarking. PMID:34458735
Comparison and Analysis on the Existing Single-Herbal Strategies against Viral Myocarditis. PMID:34456633
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. PMID:34380569
Role of Persistent Organic Pollutants in Breast Cancer Progression and Identification of Estrogen Receptor Alpha Inhibitors Using In-Silico Mining and Drug-Drug Interaction Network Approaches. PMID:34356536
Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome. PMID:34350693
Exploring the Mechanism of Scutellaria baicalensis Georgi Efficacy against Oral Squamous Cell Carcinoma Based on Network Pharmacology and Molecular Docking Analysis. PMID:34335829
In vitro and in silico analysis reveals antifungal activity and potential targets of curcumin on Paracoccidioides spp. PMID:34324170
Construction of a Virtual Opioid Bioprofile: A Data-Driven QSAR Modeling Study to Identify New Analgesic Opioids. PMID:34239782
Elucidating the Mechanism of Action of the Attributed Immunomodulatory Role of Eltrombopag in Primary Immune Thrombocytopenia: An In Silico Approach. PMID:34199099
Prognostic Biomarker-Based Identification of Drugs for Managing the Treatment of Endometrial Cancer. PMID:34155607
Fine-tuning of a generative neural network for designing multi-target compounds. PMID:34046745
Compound dataset and custom code for deep generative multi-target compound design. PMID:34046209
Structured data sets of compounds with multi-target and corresponding single-target activity from biological assays. PMID:34046190
Comparative Analysis on Single- and Multiherb Strategies in Coronary Artery Atherosclerosis Therapy. PMID:34012683
An integrative network analysis framework for identifying molecular functions in complex disorders examining major depressive disorder as a test case. PMID:33958659
Network Pharmacology and Molecular Docking Suggest the Mechanism for Biological Activity of Rosmarinic Acid. PMID:33936238
Lipidomics-Based Comparison of Molecular Compositions of Green, Yellow, and Red Bell Peppers. PMID:33919953
Schisandrol A Suppresses Catabolic Factor Expression by Blocking NF-κB Signaling in Osteoarthritis. PMID:33800441
Discovery of New Protein Targets of BPA Analogs and Derivatives Associated with Noncommunicable Diseases: A Virtual High-Throughput Screening. PMID:33769846
Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2. PMID:33669738
Deciphering potential pharmacological mechanism of Sha-Shen-Mai-Dong decoction on primary Sjogren's syndrome. PMID:33648502
Network pharmacology modeling identifies synergistic interaction of therapeutic and toxicological mechanisms for Tripterygium hypoglaucum Hutch. PMID:33446184
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. PMID:33431038
Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development. PMID:33431009
Epidrug Repurposing: Discovering New Faces of Old Acquaintances in Cancer Therapy. PMID:33312959
Analysis of Biological Screening Compounds with Single- or Multi-Target Activity via Diagnostic Machine Learning. PMID:33260876
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations. PMID:33209251
S-adenosylmethionine administration inhibits levodopa-induced vascular endothelial growth factor-A expression. PMID:33170152
Network Pharmacology and bioinformatics analyses identify intersection genes of niacin and COVID-19 as potential therapeutic targets. PMID:33169132
Network pharmacology and molecular docking analyses on Lianhua Qingwen capsule indicate Akt1 is a potential target to treat and prevent COVID-19. PMID:33140889
Network Pharmacology-Based Study on the Mechanism of Pinellia ternata in Asthma Treatment. PMID:33133221
MASI: microbiota-active substance interactions database. PMID:33125077
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
Inhibitor bias in luciferase-based luminescence assays. PMID:32983562
Prediction of Promiscuity Cliffs Using Machine Learning. PMID:32881355
UCSF ChimeraX: Structure visualization for researchers, educators, and developers. PMID:32881101
Coupled immune stratification and identification of therapeutic candidates in patients with lung adenocarcinoma. PMID:32855362
Pruned Machine Learning Models to Predict Aqueous Solubility. PMID:32685821
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
ACD: Antimicrobial chemotherapeutics database. PMID:32584882
Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement. PMID:32575564
Increasing the public activity cliff knowledge base with new categories of activity cliffs. PMID:32518687
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. PMID:32440005
Advances in exploring activity cliffs. PMID:32367387
A Chemographic Audit of anti-Coronavirus Structure-activity Information from Public Databases (ChEMBL). PMID:32363750
A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches. PMID:32322011
From SAR Diagnostics to Compound Design: Development Chronology of the Compound Optimization Monitor (COMO) Method. PMID:32282989
A Deep Learning Approach to Antibiotic Discovery. PMID:32084340
Biological Activity Profiles of Multitarget Ligands from X-ray Structures. PMID:32059498
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Identifying Synergistic Mechanisms of Multiple Ingredients in Shuangbai Tablets against Proteinuria by Virtual Screening and a Network Pharmacology Approach. PMID:32025234
Integrating Exposure Knowledge and Serum Suspect Screening as a New Approach to Biomonitoring: An Application in Firefighters and Office Workers. PMID:31971370
Combined network pharmacology and virtual reverse pharmacology approaches for identification of potential targets to treat vascular dementia. PMID:31937840
Machine and deep learning approaches for cancer drug repurposing. PMID:31904426
Current computational methods for predicting protein interactions of natural products. PMID:31762960
Identifying Promiscuous Compounds with Activity against Different Target Classes. PMID:31752252
Comprehensive investigation of the clinical significance and molecular mechanisms of plasmacytoma variant translocation 1 in sarcoma using genome-wide RNA sequencing data. PMID:31598169
Structural Modeling and in Silico Screening of Potential Small-Molecule Allosteric Agonists of a Glucagon-like Peptide 1 Receptor. PMID:31459371
Examination of molecular space and feasible structures of bioactive components of humic substances by FTICR MS data mining in ChEMBL database. PMID:31427609
Network Pharmacology-Based Pharmacological Mechanism of the Chinese Medicine Rhizoma drynariae Against Osteoporosis. PMID:31368456
Insights into Computational Drug Repurposing for Neurodegenerative Disease. PMID:31326236
Experimental evidence and network pharmacology identify the molecular targets of Tong Sheng tablets in cerebral ischemia reperfusion injury. PMID:31312345
Metabolomic Analysis Identifies Alterations of Amino Acid Metabolome Signatures in the Postmortem Brain of Alzheimer's Disease. PMID:31308797
DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences. PMID:31199797
Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry. PMID:31092576
Inhibition of Oncogenic Kinases: An In Vitro Validated Computational Approach Identified Potential Multi-Target Anticancer Compounds. PMID:30925835
Genome-scale integrated analysis to identify prospective molecular mechanisms and therapeutic targets in isocitrate dehydrogenase 2 R140Q-mutated acute myeloid leukemia. PMID:30896832
Systematic identification of target set-dependent activity cliffs. PMID:30828462
Computational Assessment of Chemical Saturation of Analogue Series under Varying Conditions. PMID:30556013
Practical Model Selection for Prospective Virtual Screening. PMID:30500183
Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction. PMID:30459617
ChEMBL: towards direct deposition of bioassay data. PMID:30398643
Database resources of the National Center for Biotechnology Information. PMID:30395293
PubChem 2019 update: improved access to chemical data. PMID:30371825
Comparison of Quantitative and Qualitative (Q)SAR Models Created for the Prediction of Ki and IC50 Values of Antitarget Inhibitors. PMID:30364128
Network-Based Methods for Prediction of Drug-Target Interactions. PMID:30356768
Enhancing Molecular Promiscuity Evaluation Through Assay Profiles. PMID:30338400
Computationally derived compound profiling matrices. PMID:30271615
Foundations of data-driven medicinal chemistry. PMID:30271612
Machine Learning for Drug-Target Interaction Prediction. PMID:30200333
Five Years of the KNIME Vernalis Cheminformatics Community Contribution. PMID:30182834
PubChem chemical structure standardization. PMID:30097821
Deep reinforcement learning for de novo drug design. PMID:30050984
Prediction of Compound Profiling Matrices Using Machine Learning. PMID:30023899
Extracting Compound Profiling Matrices from Screening Data. PMID:30023898
Computational Analysis of LOX1 Inhibition Identifies Descriptors Responsible for Binding Selectivity. PMID:30023828
Application of a New Scaffold Concept for Computational Target Deconvolution of Chemical Cancer Cell Line Screens. PMID:30023635
QEX: target-specific druglikeness filter enhances ligand-based virtual screening. PMID:29971617
Identification of drug-target interaction by a random walk with restart method on an interactome network. PMID:29897326
A guideline for reporting experimental protocols in life sciences. PMID:29868256
Data-driven analysis of biomedical literature suggests broad-spectrum benefits of culinary herbs and spices. PMID:29813110
Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease. PMID:29792714
An update on PUG-REST: RESTful interface for programmatic access to PubChem. PMID:29718389
IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics. PMID:29697364
Drug Repositioning in Glioblastoma: A Pathway Perspective. PMID:29615902
High-throughput screen of drug repurposing library identifies inhibitors of Sarcocystis neurona growth. PMID:29547840
RNA Interference (RNAi) Screening in Drosophila. PMID:29487145
Early Probe and Drug Discovery in Academia: A Minireview. PMID:29485615
Maximizing gain in high-throughput screening using conformal prediction. PMID:29468427
Decoys Selection in Benchmarking Datasets: Overview and Perspectives. PMID:29416509
CLC-Pred: A freely available web-service for in silico prediction of human cell line cytotoxicity for drug-like compounds. PMID:29370280
Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain. PMID:29321504
Metallochaperone UreG serves as a new target for design of urease inhibitor: A novel strategy for development of antimicrobials. PMID:29320492
Identification of New Potential APE1 Inhibitors by Pharmacophore Modeling and Molecular Docking. PMID:29307141
Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions. PMID:29276046
Database of resistance related metabolites in Wheat Fusarium head blight Disease (MWFD). PMID:29220474
Seven Year Itch: Pan-Assay Interference Compounds (PAINS) in 2017-Utility and Limitations. PMID:29202222
Database resources of the National Center for Biotechnology Information. PMID:29140470
NPASS: natural product activity and species source database for natural product research, discovery and tool development. PMID:29106619
Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp3 Centers Enhance Target Selectivity. PMID:28894419
Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows. PMID:28809006
Virtual Screening against Phosphoglycerate Kinase 1 in Quest of Novel Apoptosis Inhibitors. PMID:28635653
Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. PMID:28602100
On the Integration of In Silico Drug Design Methods for Drug Repurposing. PMID:28588497
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. PMID:28577120
Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer. PMID:28558972
PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing. PMID:28346087
Knocking down the obstacles to functional genomics data sharing. PMID:28248922
The ChEMBL database in 2017. PMID:27899562