BindingDB database of measured binding affinities
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BindingDB database of measured binding affinities
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
BindingDB
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
BDB
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
The Binding Database
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
bindingdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Names
More detailed information about this field from each metasource.
BindingDB database of measured binding affinities
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
BindingDB
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
BDB
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
The Binding Database
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
bindingdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
Other names: BindingDB, BDB, The Binding Database, bindingdb
Names
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BindingDB database of measured binding affinities
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
BindingDB
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
BDB
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
The Binding Database
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
bindingdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.
Description
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BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
BindingDB (http://www.bindingdb.org) curates measured binding affinities for the association ofproteins with small organic molecules. Data are drawn from thescientific literature, focusing on proteins that are known orpotential drug targets, and for which structural data is available inthe Protein Data Bank. The curated data include detailed experimentalconditions, such as pH, temperature, and solution composition.Examples of target proteins for which substantial data sets have beencollected include anthrax lethal factor, HIV protease, HIV reversetranscriptase, and various kinases and caspases. The database allowsquerying by target and compound name, target protein sequence,chemical substructure and similarity, and PubMed ID and PDB codes.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
BindingDB is a public, web-accessible knowledgebase of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules. BindingDB supports medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modeling approaches such as docking, scoring and free energy methods; chemical biology and chemical genomics; and basic studies of the physical chemistry of molecular recognition. BindingDB also includes a small collection of host-guest binding data of interest to chemists studying supramolecular systems. The data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays. BindingDB includes data extracted from the literature and from US Patents by the BindingDB project, selected PubChem confirmatory BioAssays, and ChEMBL entries for which a well defined protein target ("TARGET_TYPE='PROTEIN'") is provided.
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
Webpage:
http://www.bindingdb.orgWebpage
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http://www.bindingdb.org
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.bindingdb.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
http://bindingdb.org/bind/index.jsp
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
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Name: Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Generic (CC BY-NC-ND 2.5)Licence name
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Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Generic (CC BY-NC-ND 2.5)
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
CC
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
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https://creativecommons.org/licenses/by-nc-nd/2.5/
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
https://creativecommons.org/licenses/by/3.0/us/
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
Publications:
Publications
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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
PMID: 17145705
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkl999
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Publications
More detailed information about this field from each metasource.
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
PMID: 17145705
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkl999
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
PubMed citations: 486.
486 articles citing: BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
Reciprocal perspective as a super learner improves drug-target interaction prediction (MUSDTI). PMID:35918366
Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
Protein-Ligand Docking in the Machine-Learning Era. PMID:35889440
Identifying Possible AChE Inhibitors from Drug-like Molecules via Machine Learning and Experimental Studies. PMID:35755364
DTI-BERT: Identifying Drug-Target Interactions in Cellular Networking Based on BERT and Deep Learning Method. PMID:35754843
Mechanism of action involved in the anxiolytic-like effects of Hibalactone isolated from Hydrocotyle umbellata L. PMID:35747359
Hierarchical Virtual Screening Based on Rocaglamide Derivatives to Discover New Potential Anti-Skin Cancer Agents. PMID:35720115
How can natural language processing help model informed drug development?: a review. PMID:35702625
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
A Network Pharmacology Analysis of Cytotoxic Triterpenes Isolated from Euphorbia abyssinica Latex Supported by Drug-likeness and ADMET Studies. PMID:35664578
Multi-TransDTI: Transformer for Drug-Target Interaction Prediction Based on Simple Universal Dictionaries with Multi-View Strategy. PMID:35625572
An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway. PMID:35625318
Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. PMID:35594413
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. PMID:35579568
UnbiasedDTI: Mitigating Real-World Bias of Drug-Target Interaction Prediction by Using Deep Ensemble-Balanced Learning. PMID:35566330
Discovery of VEGFR2 inhibitors by integrating naïve Bayesian classification, molecular docking and drug screening approaches. PMID:35542432
Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. PMID:35507313
Discovery of moiety preference by Shapley value in protein kinase family using random forest models. PMID:35428180
SSGraphCPI: A Novel Model for Predicting Compound-Protein Interactions Based on Deep Learning. PMID:35409140
Repurposing Multiple-Molecule Drugs for COVID-19-Associated Acute Respiratory Distress Syndrome and Non-Viral Acute Respiratory Distress Syndrome via a Systems Biology Approach and a DNN-DTI Model Based on Five Drug Design Specifications. PMID:35409008
Predicting the binding of small molecules to nuclear receptors using machine learning. PMID:35383362
Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network. PMID:35380443
Network Pharmacology Identifies Therapeutic Targets and the Mechanisms of Glutathione Action in Ferroptosis Occurring in Oral Cancer. PMID:35359830
High-Throughput Screening Assay Profiling for Large Chemical Databases. PMID:35294761
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding. PMID:35292100
Chemogenomic Approaches for Revealing Drug Target Interactions in Drug Discovery. PMID:35283667
Discovery of Kinase and Carbonic Anhydrase Dual Inhibitors by Machine Learning Classification and Experiments. PMID:35215348
DOTA: Deep Learning Optimal Transport Approach to Advance Drug Repositioning for Alzheimer's Disease. PMID:35204697
Hepatitis C Virus NS3/4A Inhibition and Host Immunomodulation by Tannins from Terminalia chebula: A Structural Perspective. PMID:35164341
Identification of New KRAS G12D Inhibitors through Computer-Aided Drug Discovery Methods. PMID:35163234
ER/AR Multi-Conformational Docking Server: A Tool for Discovering and Studying Estrogen and Androgen Receptor Modulators. PMID:35140614
A New Prospect for the Treatment of Nephrotic Syndrome Based on Network Pharmacology Analysis. PMID:35098155
A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease. PMID:35037854
Multi-scale mechanism of antiviral drug-alike phytoligands from Ayurveda in managing COVID-19 and associated metabolic comorbidities: insights from network pharmacology. PMID:34993740
Discovery of a novel cyclin-dependent kinase 8 inhibitor with an oxindole core for anti-inflammatory treatment. PMID:34953394
Predicting New Anti-Norovirus Inhibitor With the Help of Machine Learning Algorithms and Molecular Dynamics Simulation-Based Model. PMID:34869204
Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions. PMID:34849575
DeepH-DTA: Deep Learning for Predicting Drug-Target Interactions: A Case Study of COVID-19 Drug Repurposing. PMID:34786289
ScaffComb: A Phenotype-Based Framework for Drug Combination Virtual Screening in Large-Scale Chemical Datasets. PMID:34723439
Multifaceted targeting strategies in cancer against the human notch 3 protein: a computational study. PMID:34631360
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. PMID:34623382
ABCpred: a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors. PMID:34609711
Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks. PMID:34590285
Polyphenols as alternative treatments of COVID-19. PMID:34567475
Automatic Identification of Analogue Series from Large Compound Data Sets: Methods and Applications. PMID:34500724
Machine learning methods, databases and tools for drug combination prediction. PMID:34477201
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Effective Use of Empirical Data for Virtual Screening against APJR GPCR Receptor. PMID:34443478
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3. PMID:34432238
Discovery of novel MIF inhibitors that attenuate microglial inflammatory activation by structures-based virtual screening and in vitro bioassays. PMID:34429524
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. PMID:34380569
Machine learning approaches for drug combination therapies. PMID:34368832
Novel High Affinity Sigma-1 Receptor Ligands from Minimal Ensemble Docking-Based Virtual Screening. PMID:34360878
Advances in the computational landscape for repurposed drugs against COVID-19. PMID:34339864
Host metabolic reprogramming in response to SARS-CoV-2 infection: A systems biology approach. PMID:34333072
Development of antibacterial compounds that constrain evolutionary pathways to resistance. PMID:34279221
Discovery of potential imaging and therapeutic targets for severe inflammation in COVID-19 patients. PMID:34239034
Application of Machine Learning for Drug-Target Interaction Prediction. PMID:34234813
Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems. PMID:34232033
Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors. PMID:34199858
Identification of known drugs as potential SARS-CoV-2 Mpro inhibitors using ligand- and structure-based virtual screening. PMID:34169729
Computational Investigation Identified Potential Chemical Scaffolds for Heparanase as Anticancer Therapeutics. PMID:34156395
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. PMID:34151987
Machine learning models to select potential inhibitors of acetylcholinesterase activity from SistematX: a natural products database. PMID:34132933
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
Ayurveda botanicals in COVID-19 management: An in silico multi-target approach. PMID:34115763
Pretraining model for biological sequence data. PMID:34050350
Facilitating SARS CoV-2 RNA-Dependent RNA polymerase (RdRp) drug discovery by the aid of HCV NS5B palm subdomain binders: In silico approaches and benchmarking. PMID:34015671
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. PMID:33993214
Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery. PMID:33987166
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction. PMID:33978713
Consolidation of network and experimental pharmacology to divulge the antidiabetic action of Ficus benghalensis L. bark. PMID:33968581
The peripheral and core regions of virus-host network of COVID-19. PMID:33956950
Deep Learning in Virtual Screening: Recent Applications and Developments. PMID:33922714
In Silico Identification of Small Molecules as New Cdc25 Inhibitors through the Correlation between Chemosensitivity and Protein Expression Pattern. PMID:33918281
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer. PMID:33777753
Identification of drug compounds for keloids and hypertrophic scars: drug discovery based on text mining and DeepPurpose. PMID:33708974
PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds. PMID:33672700
Integration of in silico, in vitro and ex vivo pharmacology to decode the anti-diabetic action of Ficus benghalensis L. bark. PMID:33553030
RLDOCK method for predicting RNA-small molecule binding modes. PMID:33549725
Identification of Tyrosinase Inhibitors and Their Structure-Activity Relationships via Evolutionary Chemical Binding Similarity and Structure-Based Methods. PMID:33499015
AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer's drug discovery. PMID:33441136
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. PMID:33431021
Aromatic clusters in protein-protein and protein-drug complexes. PMID:33431014
Ivermectin as a potential drug for treatment of COVID-19: an in-sync review with clinical and computational attributes. PMID:33389725
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. PMID:33347301
LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates. PMID:33292486
DeepPurpose: a deep learning library for drug-target interaction prediction. PMID:33275143
Supporting SARS-CoV-2 Papain-Like Protease Drug Discovery: In silico Methods and Benchmarking. PMID:33251185
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 medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
A review on drug repurposing applicable to COVID-19. PMID:33147623
Inhibiting CDK6 Activity by Quercetin Is an Attractive Strategy for Cancer Therapy. PMID:33134711
Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study. PMID:33111624
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
RLDOCK: A New Method for Predicting RNA-Ligand Interactions. PMID:33095555
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction. PMID:33070179
Integrating Machine Learning-Based Virtual Screening With Multiple Protein Structures and Bio-Assay Evaluation for Discovery of Novel GSK3β Inhibitors. PMID:33041806
COVID-19: molecular targets, drug repurposing and new avenues for drug discovery. PMID:33027420
Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction. PMID:32993084
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Identification of New Rofecoxib-Based Cyclooxygenase-2 Inhibitors: A Bioinformatics Approach. PMID:32858871
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
Design, Synthesis, and Biological Evaluation of Novel 7H-[1,2,4]Triazolo[3,4-b][1,3,4]thiadiazine Inhibitors as Antitumor Agents. PMID:32832771
The role of NMR in leveraging dynamics and entropy in drug design. PMID:32720098
A Network Medicine Approach to Investigation and Population-based Validation of Disease Manifestations and Drug Repurposing for COVID-19. PMID:32676577
Evolutionary chemical binding similarity approach integrated with 3D-QSAR method for effective virtual screening. PMID:32664863
Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand-Receptor Interactions. PMID:32652079
A site-moiety map and virtual screening approach for discovery of novel 5-LOX inhibitors. PMID:32601404
Comprehensive germline genomic profiles of children, adolescents and young adults with solid tumors. PMID:32371905
Computer-Driven Development of an in Silico Tool for Finding Selective Histone Deacetylase 1 Inhibitors. PMID:32331470
Fr-PPIChem: An Academic Compound Library Dedicated to Protein-Protein Interactions. PMID:32320205
Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. PMID:32280433
Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. PMID:32194980
DeltaDelta neural networks for lead optimization of small molecule potency. PMID:32190246
New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections. PMID:32184419
Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds. PMID:32162456
DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening. PMID:32035227
In Silico Strategies in Tuberculosis Drug Discovery. PMID:32033144
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. PMID:31971579
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Small-Molecule Intervention At The Dimerization Interface Of Survivin By Novel Rigidized Scaffolds. PMID:31908412
A prospective compound screening contest identified broader inhibitors for Sirtuin 1. PMID:31863054
Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities. PMID:31824921
Recognizing ion ligand binding sites by SMO algorithm. PMID:31823742
Cross-docking benchmark for automated pose and ranking prediction of ligand binding. PMID:31721338
Systematic Elucidation of the Mechanism of Genistein against Pulmonary Hypertension via Network Pharmacology Approach. PMID:31703458
Current progress and future perspectives of polypharmacology : From the view of non-small cell lung cancer. PMID:31698087
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. PMID:31677003
CavBench: A benchmark for protein cavity detection methods. PMID:31609980
Application of the Movable Type Free Energy Method to the Caspase-Inhibitor BindingAffinity Study. PMID:31569580
The perceptions of natural compounds against dipeptidyl peptidase 4 in diabetes: from in silico to in vivo. PMID:31555430
Molecular Docking: Shifting Paradigms in Drug Discovery. PMID:31487867
Artificial Intelligence for Drug Toxicity and Safety. PMID:31383376
Systems Pharmacology for Investigation of the Mechanisms of Action of Traditional Chinese Medicine in Drug Discovery. PMID:31379563
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria. PMID:31360332
Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity. PMID:31350558
Insights about multi-targeting and synergistic neuromodulators in Ayurvedic herbs against epilepsy: integrated computational studies on drug-target and protein-protein interaction networks. PMID:31332210
Bioassay Directed Isolation, Biological Evaluation and in Silico Studies of New Isolates from Pteris cretica L. PMID:31331076
Discovery and characterization of trypanocidal cysteine protease inhibitors from the 'malaria box'. PMID:31284086
Why Some Targets Benefit from beyond Rule of Five Drugs. PMID:31188592
Drug repositioning of herbal compounds via a machine-learning approach. PMID:31138103
Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. PMID:31125569
Repurposing of FDA-Approved NSAIDs for DPP-4 Inhibition as an Alternative for Diabetes Mellitus Treatment: Computational and in Vitro Study. PMID:31108878
The carboxy-terminus, a key regulator of protein function. PMID:31106589
Identification of a Novel Bcl-2 Inhibitor by Ligand-Based Screening and Investigation of Its Anti-cancer Effect on Human Breast Cancer Cells. PMID:31057406
Epigenetic Modulators as Potential Multi-targeted Drugs Against Hedgehog Pathway for Treatment of Cancer. PMID:30993446
A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data. PMID:30988527
Untargeted Metabolomics Study of the In Vitro Anti-Hepatoma Effect of Saikosaponin d in Combination with NRP-1 Knockdown. PMID:30978940
Structure Based Design and Molecular Docking Studies for Phosphorylated Tau Inhibitors in Alzheimer's Disease. PMID:30893872
Network-based prediction of drug combinations. PMID:30867426
Hybrid approach to sieve out natural compounds against dual targets in Alzheimer's Disease. PMID:30842555
Discovery of Novel Acetylcholinesterase Inhibitors as Potential Candidates for the Treatment of Alzheimer's Disease. PMID:30823604
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. PMID:30768156
In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics. PMID:30754680
A Novel Discovery: Holistic Efficacy at the Special Organ Level of Pungent Flavored Compounds from Pungent Traditional Chinese Medicine. PMID:30754631
The Phenolic compound Kaempferol overcomes 5-fluorouracil resistance in human resistant LS174 colon cancer cells. PMID:30655588
Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays. PMID:30639122
Identification of potential drug targets and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic approach. PMID:30607324
A Novel Selective JAK2 Inhibitor Identified Using Pharmacological Interactions. PMID:30564118
Combining a QSAR Approach and Structural Analysis to Derive an SAR Map of Lyn Kinase Inhibition. PMID:30544914
Discovery of Non-Peptidic Compounds against Chagas Disease Applying Pharmacophore Guided Molecular Modelling Approaches. PMID:30469538
Implicit-descriptor ligand-based virtual screening by means of collaborative filtering. PMID:30467684
Systems-Mapping of Herbal Effects on Complex Diseases Using the Network-Perturbation Signatures. PMID:30405409
High-throughput screening for selective appetite modulators: A multibehavioral and translational drug discovery strategy. PMID:30402545
In search of the representative pharmacophore hypotheses of the enzymatic proteome of Plasmodium falciparum: a multicomplex-based approach. PMID:30315397
Development of comprehensive data repository on chemicals present in smokeless tobacco products: Opportunities & challenges. PMID:30264748
Potential use of compounds from sea cucumbers as MDM2 and CXCR4 inhibitors to control cancer cell growth. PMID:30250516
Target-based drug discovery through inversion of quantitative structure-drug-property relationships and molecular simulation: CA IX-sulphonamide complexes. PMID:30220229
Machine Learning for Drug-Target Interaction Prediction. PMID:30200333
eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database. PMID:30052959
KampoDB, database of predicted targets and functional annotations of natural medicines. PMID:30046160
Compound Ranking Based on Fuzzy Three-Dimensional Similarity Improves the Performance of Docking into Homology Models of G-Protein-Coupled Receptors. PMID:30023670
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
In silico approach in reveal traditional medicine plants pharmacological material basis. PMID:29946351
Interspecies comparison of putative ligand binding sites of human, rat and mouse P-glycoprotein. PMID:29936088
Identification of Estrogen Receptor α Antagonists from Natural Products via In Vitro and In Silico Approaches. PMID:29861831
High-Throughput Screening Assay Datasets from the PubChem Database. PMID:29795804
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach. PMID:29732444
SPIDR: small-molecule peptide-influenced drug repurposing. PMID:29661129
Uncovering the Mechanisms of Chinese Herbal Medicine (MaZiRenWan) for Functional Constipation by Focused Network Pharmacology Approach. PMID:29632490
Docking-based inverse virtual screening: methods, applications, and challenges. PMID:29577065
TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds. PMID:29520288
Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain. PMID:29321504
A census of P. longum's phytochemicals and their network pharmacological evaluation for identifying novel drug-like molecules against various diseases, with a special focus on neurological disorders. PMID:29320554
Predicting inhibitory and activatory drug targets by chemically and genetically perturbed transcriptome signatures. PMID:29317676
Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening. PMID:29306979
Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection. PMID:29297305
Thiopurine Drugs Repositioned as Tyrosinase Inhibitors. PMID:29283382
Computational Exploration for Lead Compounds That Can Reverse the Nuclear Morphology in Progeria. PMID:29226142
TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. PMID:29220433
Computational approaches to chemical hazard assessment. PMID:29101769
Antithrombotic properties of JJ1, a potent and novel thrombin inhibitor. PMID:29093471
From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets. PMID:28986673
An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. PMID:28931921
PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets. PMID:28931422
In silico prediction of ROCK II inhibitors by different classification approaches. PMID:28770474
Virtual Screening and Statistical Analysis in the Design of New Caffeine Analogues Molecules with Potential Epithelial Anticancer Activity. PMID:28699538
A simple mathematical approach to the analysis of polypharmacology and polyspecificity data. PMID:28690829
Predicting the Reliability of Drug-target Interaction Predictions with Maximum Coverage of Target Space. PMID:28630414
AlzhCPI: A knowledge base for predicting chemical-protein interactions towards Alzheimer's disease. PMID:28542505
Assessing protein-ligand binding modes with computational tools: the case of PDE4B. PMID:28534194
Repurposing of Proton Pump Inhibitors as first identified small molecule inhibitors of endo-β-N-acetylglucosaminidase (ENGase) for the treatment of NGLY1 deficiency, a rare genetic disease. PMID:28512024
Receptor-ligand molecular docking. PMID:28509958
Computational design of ligand-binding membrane receptors with high selectivity. PMID:28459439
Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory. PMID:28453640
Rational design of non-resistant targeted cancer therapies. PMID:28436422
Improving the accuracy of high-throughput protein-protein affinity prediction may require better training data. PMID:28361672
Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. PMID:28274840
Chemical Space Mimicry for Drug Discovery. PMID:28257191
Insights into the molecular mechanisms of Polygonum multiflorum Thunb-induced liver injury: a computational systems toxicology approach. PMID:28239160
Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. PMID:28233410
Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. PMID:28150250
Protein Bioinformatics Databases and Resources. PMID:28150231
Prediction of kinase-inhibitor binding affinity using energetic parameters. PMID:28149052
Computational methods in drug discovery. PMID:28144341
3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. PMID:28125221
Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors. PMID:28108896
Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics. PMID:28071740
In Silico Exploration for Novel Type-I Inhibitors of Tie-2/TEK: The Performance of Different Selection Strategy in Selecting Virtual Screening Candidates. PMID:27876862
Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. PMID:27736015
Improved pose and affinity predictions using different protocols tailored on the basis of data availability. PMID:27714493
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. PMID:27696240
In silico prediction of chemical mechanism of action via an improved network-based inference method. PMID:27646592
Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds. PMID:27530612
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets. PMID:27515740
MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors. PMID:27509041
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PMID:27467583
New ursane triterpenoids from Ficus pandurata and their binding affinity for human cannabinoid and opioid receptors. PMID:27350550
Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor. PMID:27334985
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. PMID:27330567
Literature information in PubChem: associations between PubChem records and scientific articles. PMID:27293485
Lead identification for the K-Ras protein: virtual screening and combinatorial fragment-based approaches. PMID:27217775
TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models. PMID:27167132
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. PMID:27151405
systemsDock: a web server for network pharmacology-based prediction and analysis. PMID:27131384
MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs. PMID:27131358
Exploring the chemical space of influenza neuraminidase inhibitors. PMID:27114890
Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery. PMID:27102549
A new molecular signature method for prediction of driver cancer pathways from transcriptional data. PMID:27098033
Stacking with No Planarity? PMID:27096037
Fragment oriented molecular shapes. PMID:27085751
Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach. PMID:27083051
In silico methods for drug repurposing and pharmacology. PMID:27080087
Modern approaches to accelerate discovery of new antischistosomal drugs. PMID:27073973
Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors. PMID:27034268
A web server for analysis, comparison and prediction of protein ligand binding sites. PMID:27016210
Drug Repositioning for Cancer Therapy Based on Large-Scale Drug-Induced Transcriptional Signatures. PMID:26954019
ChemProt-3.0: a global chemical biology diseases mapping. PMID:26876982
Theoretical Study of Molecular Structure and Physicochemical Properties of Novel Factor Xa Inhibitors and Dual Factor Xa and Factor IIa Inhibitors. PMID:26861270
Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking. PMID:26845440
Understanding TRPV1 activation by ligands: Insights from the binding modes of capsaicin and resiniferatoxin. PMID:26719417
Biocuration with insufficient resources and fixed timelines. PMID:26708987
High-throughput screening against ~6.1 million structurally diverse, lead-like compounds to discover novel ROCK inhibitors for cerebral injury recovery. PMID:26700101
Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. PMID:26696900
Fundamentals of protein interaction network mapping. PMID:26681426
Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach. PMID:26677339
Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach. PMID:26657081
ONRLDB--manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery. PMID:26637529
Repositioning of Thiourea-Containing Drugs as Tyrosinase Inhibitors. PMID:26633377
Drug target prioritization by perturbed gene expression and network information. PMID:26615774
Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. PMID:26607293
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. PMID:26578601
Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays. PMID:26568382
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. PMID:26481362
ZINC 15--Ligand Discovery for Everyone. PMID:26479676
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. PMID:26464438
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. PMID:26442281
In silico exploration of c-KIT inhibitors by pharmaco-informatics methodology: pharmacophore modeling, 3D QSAR, docking studies, and virtual screening. PMID:26416560
PubChem Substance and Compound databases. PMID:26400175
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. PMID:26384374
Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data. PMID:26376645
Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy. PMID:26370248
Screening Ingredients from Herbs against Pregnane X Receptor in the Study of Inductive Herb-Drug Interactions: Combining Pharmacophore and Docking-Based Rank Aggregation. PMID:26339628
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Navigating the chemical space of dipeptidyl peptidase-4 inhibitors. PMID:26309399
RepurposeVS: A Drug Repurposing-Focused Computational Method for Accurate Drug-Target Signature Predictions. PMID:26234515
New Frontiers in Druggability. PMID:26230724
PhIN: A Protein Pharmacology Interaction Network Database. PMID:26225242
Molecular docking and structure-based drug design strategies. PMID:26205061
Activity, assay and target data curation and quality in the ChEMBL database. PMID:26201396
Expanding opportunities for mining bioactive chemistry from patents. PMID:26194581
Large-scale structure-activity relationship study of hepatitis C virus NS5B polymerase inhibition using SMILES-based descriptors. PMID:26164590
Large-scale Direct Targeting for Drug Repositioning and Discovery. PMID:26155766
Activity cliffs and activity cliff generators based on chemotype-related activity landscapes. PMID:26150300
Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. PMID:26121262
Combinatorial Pharmacophore-Based 3D-QSAR Analysis and Virtual Screening of FGFR1 Inhibitors. PMID:26110383
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
Building a virtual ligand screening pipeline using free software: a survey. PMID:26094053
Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. PMID:26091166
Many InChIs and quite some feat. PMID:26081259
Anchor-based classification and type-C inhibitors for tyrosine kinases. PMID:26077136
Design and Validation of FRESH, a Drug Discovery Paradigm Resting on Robust Chemical Synthesis. PMID:26005525
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. PMID:25971743
Structure-based predictions of activity cliffs. PMID:25918827
Predicting drug metabolism: experiment and/or computation? PMID:25907346
ChEMBL web services: streamlining access to drug discovery data and utilities. PMID:25883136
Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. PMID:25692383
Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. PMID:25690787
Computational polypharmacology analysis of the heat shock protein 90 interactome. PMID:25686391
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
A ranking method for the concurrent learning of compounds with various activity profiles. PMID:25643067
Introducing the 'active search' method for iterative virtual screening. PMID:25636815
A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity. PMID:25555059
Follow up: Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer. PMID:25520777
Consensus models for CDK5 inhibitors in silico and their application to inhibitor discovery. PMID:25511641
Benchmarking methods and data sets for ligand enrichment assessment in virtual screening. PMID:25481478
A chemo-centric view of human health and disease. PMID:25435099
Parallel worlds of public and commercial bioactive chemistry data. PMID:25415348
Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. PMID:25414519
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. PMID:25378330
T3DB: the toxic exposome database. PMID:25378312
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. PMID:25324307
Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. PMID:25284249
A document classifier for medicinal chemistry publications trained on the ChEMBL corpus. PMID:25221627
Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology. PMID:25205292
Human structural proteome-wide characterization of Cyclosporine A targets. PMID:25172926
An in silico protocol for identifying mTOR inhibitors from natural products. PMID:25156384
Curation and analysis of multitargeting agents for polypharmacological modeling. PMID:25133604
The Protein Data Bank archive as an open data resource. PMID:25062767
In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion. PMID:24976868
Testing the sensitivities of noncognate inhibitors to varicella zoster virus thymidine kinase: implications for postherpetic neuralgia therapy with existing agents. PMID:24961898
iDrug: a web-accessible and interactive drug discovery and design platform. PMID:24955134
Chemical transformations that yield compounds with distinct activity profiles. PMID:24900343
Thermodynamics of ligand binding and efficiency. PMID:24900326
Extracting SAR Information from a Large Collection of Anti-Malarial Screening Hits by NSG-SPT Analysis. PMID:24900303
Exploring target-selectivity patterns of molecular scaffolds. PMID:24900176
Atom-based 3D-QSAR, molecular docking and molecular dynamics simulation assessment of inhibitors for thyroid hormone receptor α and β. PMID:24898938
VAV3 mediates resistance to breast cancer endocrine therapy. PMID:24886537
SuperPred: update on drug classification and target prediction. PMID:24878925
ProTox: a web server for the in silico prediction of rodent oral toxicity. PMID:24838562
Predicting mTOR inhibitors with a classifier using recursive partitioning and Naïve Bayesian approaches. PMID:24819222
PLIC: protein-ligand interaction clusters. PMID:24763918
Integrated computational tools for identification of CCR5 antagonists as potential HIV-1 entry inhibitors: homology modeling, virtual screening, molecular dynamics simulations and 3D QSAR analysis. PMID:24762964
Chemical, target, and bioactive properties of allosteric modulation. PMID:24699297
Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. PMID:24699146
Network-assisted prediction of potential drugs for addiction. PMID:24689033
VNP: Interactive Visual Network Pharmacology of Diseases, Targets, and Drugs. PMID:24622768
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
Development of a human dihydroorotate dehydrogenase (hDHODH) pharma-similarity index approach with scaffold-hopping strategy for the design of novel potential inhibitors. PMID:24504131
The role of ligand efficiency metrics in drug discovery. PMID:24481311
Drug targets for cell cycle dysregulators in leukemogenesis: in silico docking studies. PMID:24454966
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 of distant drug off-targets by direct superposition of binding pocket surfaces. PMID:24391782
Exploration of virtual candidates for human HMG-CoA reductase inhibitors using pharmacophore modeling and molecular dynamics simulations. PMID:24386216
Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications. PMID:24358818
Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors. PMID:24335842
An efficient multistep ligand-based virtual screening approach for GPR40 agonists. PMID:24307222
Predicting drug-target interactions using drug-drug interactions. PMID:24278248
SuperPain--a resource on pain-relieving compounds targeting ion channels. PMID:24271391
The Reactome pathway knowledgebase. PMID:24243840
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. PMID:24234439
A comprehensive survey of small-molecule binding pockets in proteins. PMID:24204237
DrugBank 4.0: shedding new light on drug metabolism. PMID:24203711
Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. PMID:24189400
Modeling protein-peptide recognition based on classical quantitative structure-affinity relationship approach: implication for proteome-wide inference of peptide-mediated interactions. PMID:24150505
Prediction of the P. falciparum target space relevant to malaria drug discovery. PMID:24146604
DGIdb: mining the druggable genome. PMID:24122041
Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules. PMID:24070451
Novel drug-regulated transcriptional networks in brain reveal pharmacological properties of psychotropic drugs. PMID:24010892
Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PMID:23805191
Predicting the protein targets for athletic performance-enhancing substances. PMID:23800040
AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. PMID:23792207
Chemical informatics and the drug discovery knowledge pyramid. PMID:23782037
Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome. PMID:23754939
Interplay of physics and evolution in the likely origin of protein biochemical function. PMID:23690621
Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. PMID:23654303
Use of natural products as chemical library for drug discovery and network pharmacology. PMID:23638153
CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. PMID:23617227
Comparability of mixed IC₅₀ data - a statistical analysis. PMID:23613770
Genome-scale screening of drug-target associations relevant to Ki using a chemogenomics approach. PMID:23577055
PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery. PMID:23548981
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
Informatics confronts drug-drug interactions. PMID:23414686
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
An efficient piecewise linear model for predicting activity of caspase-3 inhibitors. PMID:23351435
Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening. PMID:23342998
Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account. PMID:23296990
Multiple virtual screening approaches for finding new hepatitis C virus RNA-dependent RNA polymerase inhibitors: structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors. PMID:23282180
Polypharmacology: drug discovery for the future. PMID:23272792
Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening. PMID:23259763
Virtual screening of specific insulin-like growth factor 1 receptor (IGF1R) inhibitors from the National Cancer Institute (NCI) molecular database. PMID:23242155
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
ChemProt-2.0: visual navigation in a disease chemical biology database. PMID:23185041
Development and experimental test of support vector machines virtual screening method for searching Src inhibitors from large compound libraries. PMID:23173901
C²Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships. PMID:23134618
Discriminating of ATP competitive Src kinase inhibitors and decoys using self-organizing map and support vector machine. PMID:23117252
Enzyme informatics. PMID:23116471
Compound activity prediction using models of binding pockets or ligand properties in 3D. PMID:23116466
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. PMID:23087378
IUPHAR-DB: updated database content and new features. PMID:23087376
Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (Part II): in silico prediction in antidiabetic extracts. PMID:23028712
Exploring chemical space for drug discovery using the chemical universe database. PMID:23019491
Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (part I): virtual screening and activity assays. PMID:22984596
Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE). PMID:22925713
Computational drug discovery. PMID:22922346
An alphabetic code based atomic level molecular similarity search in databases. PMID:22829718
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. PMID:22798729
AtlasCBS: a web server to map and explore chemico-biological space. PMID:22798082
ChromoHub: a data hub for navigators of chromatin-mediated signalling. PMID:22718786
A leap into the chemical space of protein-protein interaction inhibitors. PMID:22650260
PocketAnnotate: towards site-based function annotation. PMID:22618878
LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. PMID:22594624
ZINC: a free tool to discover chemistry for biology. PMID:22587354
A chemocentric approach to the identification of cancer targets. PMID:22558171
A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. PMID:22476577
3D-QSAR studies of dihydropyrazole and dihydropyrrole derivatives as inhibitors of human mitotic kinesin Eg5 based on molecular docking. PMID:22343406
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. PMID:22210869
TDR Targets: a chemogenomics resource for neglected diseases. PMID:22116064
ProtChemSI: a network of protein-chemical structural interactions. PMID:22110041
Discovery of a novel and potent class of F. tularensis enoyl-reductase (FabI) inhibitors by molecular shape and electrostatic matching. PMID:22098466
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
SuperTarget goes quantitative: update on drug-target interactions. PMID:22067455
Classification of scaffold-hopping approaches. PMID:22056715
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. PMID:21948793
ChEMBL: a large-scale bioactivity database for drug discovery. PMID:21948594
Cross-pharmacology analysis of G protein-coupled receptors. PMID:21851335
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. PMID:21728306
Software and resources for computational medicinal chemistry. PMID:21707404
Exploiting PubChem for Virtual Screening. PMID:21691435
BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states. PMID:21600047
ChemMine tools: an online service for analyzing and clustering small molecules. PMID:21576229
Combinations of protein-chemical complex structures reveal new targets for established drugs. PMID:21573205
Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds. PMID:21569515
Ligand Identification Scoring Algorithm (LISA). PMID:21561101
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays. PMID:21390216
A machine learning-based method to improve docking scoring functions and its application to drug repurposing. PMID:21291174
Discriminating of HMG-CoA reductase inhibitors and decoys using self-organizing maps. PMID:21072588
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. PMID:21059682
The chemical basis of pharmacology. PMID:21058655
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities. PMID:21051336
The RCSB Protein Data Bank: redesigned web site and web services. PMID:21036868
Docking validation resources: protein family and ligand flexibility experiments. PMID:21033739
PubChem as a public resource for drug discovery. PMID:20970519
ChemProt: a disease chemical biology database. PMID:20935044
Higher throughput calorimetry: opportunities, approaches and challenges. PMID:20888754
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. PMID:20853887
Integration-mediated prediction enrichment of quantitative model for Hsp90 inhibitors as anti-cancer agents: 3D-QSAR study. PMID:20740314
Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies. PMID:20724439
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. PMID:20478034
Application of kernel functions for accurate similarity search in large chemical databases. PMID:20438655
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. PMID:20430828
GPM: A Graph Pattern Matching Kernel with Diffusion for Chemical Compound Classification. PMID:20428463
G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases. PMID:20428322
Combining docking with pharmacophore filtering for improved virtual screening. PMID:20298524
Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds. PMID:20298516
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. PMID:20160879
Practical application of bioinformatics by the multidisciplinary VIZIER consortium. PMID:20153379
An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery. PMID:20135687
A side effect resource to capture phenotypic effects of drugs. PMID:20087340
An overview of the PubChem BioAssay resource. PMID:19933261
STITCH 2: an interaction network database for small molecules and proteins. PMID:19897548
Structure and signaling mechanism of Per-ARNT-Sim domains. PMID:19836329
Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins. PMID:19823588
Target fishing for chemical compounds using target-ligand activity data and ranking based methods. PMID:19764745
Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. PMID:19703025
Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. PMID:19609266
Titration calorimetry standards and the precision of isothermal titration calorimetry data. PMID:19582227
Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site. PMID:19533373
PubChem: a public information system for analyzing bioactivities of small molecules. PMID:19498078
Structural models in the assessment of protein druggability based on HTS data. PMID:19479324
Robust optimization of scoring functions for a target class. PMID:19471858
Docking study of triphenylphosphonium cations as estrogen receptor alpha modulators. PMID:19293997
Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory. PMID:19217848
Directed discovery of agents targeting the Met tyrosine kinase domain by virtual screening. PMID:19199650
Mechanisms of drug combinations: interaction and network perspectives. PMID:19180105
Host-guest complexes with protein-ligand-like affinities: computational analysis and design. PMID:19133781
IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. PMID:18948278
Human immunodeficiency virus type 1, human protein interaction database at NCBI. PMID:18927109
An improved scoring function for suboptimal polar ligand complexes. PMID:18843450
Community benchmarks for virtual screening. PMID:18273555
Protein databases on the internet. PMID:18265344
Binding MOAD, a high-quality protein-ligand database. PMID:18055497
ChemBank: a small-molecule screening and cheminformatics resource database. PMID:17947324
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
Integrating physical and genetic maps: from genomes to interaction networks. PMID:17703239 - http://dx.doi.org/10.1093/nar/gkl999
Tags:
Tags
More detailed information about this field from each metasource.
affinity
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
drug binding
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
drug interaction
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein properties
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
enzymes and enzyme nomenclature
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
binding affinity
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
chemical genomics
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
drug
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
drug discovery
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
drug target
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
interaction
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
medicinal chemistry
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
small molecule
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
small molecule-protein interaction
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Tags
More detailed information about this field from each metasource.
affinity
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
drug binding
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
drug interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: BindingDB; BindingDB database of measured binding affinities; DOI: https://doi.org/10.25504/FAIRsharing.3b36hk; Last edited: Dec. 27, 2020, 8:27 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein properties
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
enzymes and enzyme nomenclature
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
binding affinity
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
chemical genomics
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
drug
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
drug discovery
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
drug target
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
interaction
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
medicinal chemistry
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
small molecule
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
small molecule-protein interaction
metasource: re3data.orgversion: re3data.org: BindingDB; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZS9T last accessed: 2022-11-04
protein interactions
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
small molecules
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
affinity binding site drug binding drug interaction protein protein interaction protein sequence protein properties metabolic and signaling pathways enzymes and enzyme nomenclature binding affinity chemical genomics drug drug discovery drug target interaction medicinal chemistry small molecule small molecule-protein interaction protein interaction small molecule
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