R3606X last accessed: 2022-11-04

stitch
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

Other names: STITCH, STITCH 4.0, stitch

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

Webpage:

http://stitch.embl.de

Licence:

Name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
URL: https://creativecommons.org/licenses/by-nc-sa/4.0/

Publications:

Publications
More detailed information about this field from each metasource.

STITCH: interaction networks of chemicals and proteins
PMID: 18084021
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

STITCH 4: integration of protein-chemical interactions with user data
PMID: 24293645
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

STITCH 3: zooming in on protein-chemical interactions
PMID: 22075997
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

STITCH 2: an interaction network database for small molecules and proteins
PMID: 19897548
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

http://dx.doi.org/10.1093/nar/gkt1207
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

STITCH: interaction networks of chemicals and proteins PubMed citations: 270.

270 articles citing: STITCH: interaction networks of chemicals and proteins

Extracellular Vesicles Derived from Early and Late Stage Plasmodium falciparum-Infected Red Blood Cells Contain Invasion-Associated Proteins. PMID:35888014
Comprehensive Computational Analysis of Honokiol Targets for Cell Cycle Inhibition and Immunotherapy in Metastatic Breast Cancer Stem Cells. PMID:35845599
Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference. PMID:35817308
Network Pharmacology Experiments Show That Emodin Can Exert a Protective Effect on MCAO Rats by Regulating Hif-1α/VEGF-A Signaling. PMID:35811865
SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19. PMID:35784208
Insights into potential mechanisms of asthma patients with COVID-19: A study based on the gene expression profiling of bronchoalveolar lavage fluid. PMID:35751199
Discovery of a Multifunctional Octapeptide from Lingzhi with Antioxidant and Tyrosinase Inhibitory Activity. PMID:35745603
Innovative in Silico Approaches for Characterization of Genes and Proteins. PMID:35664302
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
A Clinical Trial of the Effects of a Dietary Pattern on Health Metrics and Fecal Metabolites in Volunteers With Risk of Cardiovascular Disease. PMID:35619960
Discovery of new drug indications for COVID-19: A drug repurposing approach. PMID:35609015
Glabridin, a bioactive component of licorice, ameliorates diabetic nephropathy by regulating ferroptosis and the VEGF/Akt/ERK pathways. PMID:35596156
Drug-Drug Interactions Prediction Using Fingerprint Only. PMID:35586666
Antibodies Against Phosphorylcholine Among 60-Year-Olds: Clinical Role and Simulated Interactions. PMID:35479288
Network pharmacology-based analysis for unraveling potential cancer-related molecular targets of Egyptian propolis phytoconstituents accompanied with molecular docking and in vitro studies. PMID:35423607
SSGraphCPI: A Novel Model for Predicting Compound-Protein Interactions Based on Deep Learning. PMID:35409140
Metabolomic Profiling of Respiratory Muscles and Lung in Response to Long-Term Controlled Mechanical Ventilation. PMID:35392172
Acyl-CoA Binding Domain Containing 4 Polymorphism rs4986172 and Expression Can Serve as Overall Survival Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma Patients After Hepatectomy. PMID:35378899
A network biology approach to identify crucial host targets for COVID-19. PMID:35364279
Chemogenomic Approaches for Revealing Drug Target Interactions in Drug Discovery. PMID:35283667
Procyanidin B2 inhibits angiogenesis and cell growth in oral squamous cell carcinoma cells through the vascular endothelial growth factor (VEGF)/VEGF receptor 2 (VEGFR2) pathway. PMID:35220896
Molecularly Guided Drug Repurposing for Cholangiocarcinoma: An Integrative Bioinformatic Approach. PMID:35205315
Negative Modulation of the Angiogenic Cascade Induced by Allosteric Kinesin Eg5 Inhibitors in a Gastric Adenocarcinoma In Vitro Model. PMID:35164221
Intratumor genetic heterogeneity and clonal evolution to decode endometrial cancer progression. PMID:35145232
Salvia miltiorrhiza Bge. (Danshen) for Inflammatory Bowel Disease: Clinical Evidence and Network Pharmacology-Based Strategy for Developing Supplementary Medical Application. PMID:35126100
Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana. PMID:35003157
Impact of Qi-Invigorating Traditional Chinese Medicines on Diffuse Large B Cell Lymphoma Based on Network Pharmacology and Experimental Validation. PMID:34955857
Molecular identification and biological control of Ralstonia solanacearum from wilt of papaya by natural compounds and Bacillus subtilis: An integrated experimental and computational study. PMID:34866997
BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution. PMID:34849567
Classification and Functional Analysis between Cancer and Normal Tissues Using Explainable Pathway Deep Learning through RNA-Sequencing Gene Expression. PMID:34768960
Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia. PMID:34760363
Differential gene expression-based connectivity mapping identified novel drug candidate and improved Temozolomide efficacy for Glioblastoma. PMID:34696786
Targeting cathepsins: A potential link between COVID-19 and associated neurological manifestations. PMID:34604555
Etomidate inhibits cell proliferation and induces apoptosis in A549 non-small cell lung cancer cells via downregulating WWP2. PMID:34603522
Repurposing new drug candidates and identifying crucial molecules underlying PCOS Pathogenesis Based On Bioinformatics Analysis. PMID:34480296
Network Pharmacology Approach for Predicting Targets of Zishen Yutai Pills on Premature Ovarian Insufficiency. PMID:34394393
Environmental impacts of COVID-19 treatment: Toxicological evaluation of azithromycin and hydroxychloroquine in adult zebrafish. PMID:34380260
Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome. PMID:34350693
Effects of Atorvastatin on T-Cell Activation and Apoptosis in Systemic Lupus Erythematosus and Novel Simulated Interactions With C-Reactive Protein and Interleukin 6. PMID:34302321
Integrative bioinformatics approaches to map key biological markers and therapeutic drugs in Extramammary Paget's disease of the scrotum. PMID:34292991
DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment. PMID:34257842
Application of Machine Learning for Drug-Target Interaction Prediction. PMID:34234813
Toward a Coronavirus Knowledge Graph. PMID:34209818
Identification of genes modulated by interferon gamma in breast cancer cells. PMID:34189281
Combination of network and molecule structure accurately predicts competitive inhibitory interactions. PMID:34136091
Predicting anticancer hyperfoods with graph convolutional networks. PMID:34099048
Pharmacogenomic considerations for repurposing of dexamethasone as a potential drug against SARS-CoV-2 infection. PMID:34086487
Investigation of the Multi-Target Mechanism of Guanxin-Shutong Capsule in Cerebrovascular Diseases: A Systems Pharmacology and Experimental Assessment. PMID:34054530
Pretraining model for biological sequence data. PMID:34050350
Identification and validation of signal recognition particle 14 as a prognostic biomarker predicting overall survival in patients with acute myeloid leukemia. PMID:33985510
The differences in SARS-CoV and SARS-CoV-2 specific co-expression network mediated biological process in human gut enterocytes. PMID:33957338
Deep learning integration of molecular and interactome data for protein-compound interaction prediction. PMID:33933121
Bioinformatics and In Vitro Studies Reveal the Importance of p53, PPARG and Notch Signaling Pathway in Inhibition of Breast Cancer Stem Cells by Hesperetin. PMID:33880358
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders. PMID:33879050
SeBioGraph: Semi-supervised Deep Learning for the Graph via Sustainable Knowledge Transfer. PMID:33867966
Targeting AKT/mTOR and Bcl-2 for Autophagic and Apoptosis Cell Death in Lung Cancer: Novel Activity of a Polyphenol Compound. PMID:33805467
Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication. PMID:33784499
Balancing Data on Deep Learning-Based Proteochemometric Activity Classification. PMID:33779173
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
Decoding the Mechanism of Huanglian Jiedu Decoction in Treating Pneumonia Based on Network Pharmacology and Molecular Docking. PMID:33681222
Functional genomic analyses highlight a shift in Gpr17-regulated cellular processes in oligodendrocyte progenitor cells and underlying myelin dysregulation in the aged mouse cerebrum. PMID:33675110
A Multi-Omics Study Revealing the Metabolic Effects of Estrogen in Liver Cancer Cells HepG2. PMID:33672651
Potential Molecular Mechanism of TNF Superfamily-Related Genes in Glioblastoma Multiforme Based on Transcriptome and Epigenome. PMID:33643183
Identification of potential therapeutic target of naringenin in breast cancer stem cells inhibition by bioinformatics and in vitro studies. PMID:33603536
Integration of metabolomics and transcriptomics reveals convergent pathways driving radiation-induced salivary gland dysfunction. PMID:33522389
Novel Metabolic Signatures of Prostate Cancer Revealed by 1H-NMR Metabolomics of Urine. PMID:33498542
iMPTCE-Hnetwork: A Multilabel Classifier for Identifying Metabolic Pathway Types of Chemicals and Enzymes with a Heterogeneous Network. PMID:33488764
In Silico Analysis of Possible Interaction between Host Genomic Transcription Factors (TFs) and Zika Virus (ZikaSPH2015) Strain with Combinatorial Gene Regulation; Virus Versus Host-The Game Reloaded. PMID:33466592
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
Systems Pharmacology-Based Identification of Mechanisms of Action of Bolbostemma paniculatum for the Treatment of Hepatocellular Carcinoma. PMID:33436534
SmartGraph: a network pharmacology investigation platform. PMID:33430980
Effect of a Traditional Chinese Medicine Formula (CoTOL) on Serum Uric Acid and Intestinal Flora in Obese Hyperuricemic Mice Inoculated with Intestinal Bacteria. PMID:33424995
Brain Disease Network Analysis to Elucidate the Neurological Manifestations of COVID-19. PMID:33409839
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Autophagy and apoptosis induction by sesamin in MOLT-4 and NB4 leukemia cells. PMID:33262824
Betulinic Acid Exerts Cytoprotective Activity on Zika Virus-Infected Neural Progenitor Cells. PMID:33251156
TREAP: A New Topological Approach to Drug Target Inference. PMID:33129831
Functional network analysis reveals potential repurposing of β-blocker atenolol for pancreatic cancer therapy. PMID:33098056
Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. PMID:33048460
Pro-myogenic small molecules revealed by a chemical screen on primary muscle stem cells. PMID:33036659
A SARS-CoV-2 host infection model network based on genomic human Transcription Factors (TFs) depletion. PMID:32984567
Systems pharmacological study illustrates the immune regulation, anti-infection, anti-inflammation, and multi-organ protection mechanism of Qing-Fei-Pai-Du decoction in the treatment of COVID-19. PMID:32978039
Prediction of drug-target interactions from multi-molecular network based on LINE network representation method. PMID:32894154
A Bioinformatics Research on Novel Mechanism of Compound Kushen Injection for Treating Breast Cancer by Network Pharmacology and Molecular Docking Verification. PMID:32849897
Medicinal Properties of Lilium candidum L. and Its Phytochemicals. PMID:32751398
Matrix metallopeptidase 9 as a host protein target of chloroquine and melatonin for immunoregulation in COVID-19: A network-based meta-analysis. PMID:32679150
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective. PMID:32599245
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
Insights into Substrate and Inhibitor Selectivity among Human GLUT Transporters through Comparative Modeling and Molecular Docking. PMID:32462103
Prediction of Drug Side Effects with a Refined Negative Sample Selection Strategy. PMID:32454877
In silico analysis of functional linkage among arsenic induced MATE genes in rice. PMID:32435604
Combining data integration and molecular dynamics for target identification in α-Synuclein-aggregating neurodegenerative diseases: Structural insights on Synaptojanin-1 (Synj1). PMID:32419904
Study on the Antibreast Cancer Mechanism and Bioactive Components of Si-Wu-Tang by Cell Type-Specific Molecular Network. PMID:32256636
The potential drug for treatment in pancreatic adenocarcinoma: a bioinformatical study based on distinct drug databases. PMID:32206083
Deciphering the Active Compounds and Mechanisms of Qixuehe Capsule on Qi Stagnation and Blood Stasis Syndrome: A Network Pharmacology Study. PMID:32190085
A Novel Approach for Drug-Target Interactions Prediction Based on Multimodal Deep Autoencoder. PMID:32047432
Inferring new relations between medical entities using literature curated term co-occurrences. PMID:31984370
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
A network pharmacology approach to reveal the protective mechanism of Salvia miltiorrhiza-Dalbergia odorifera coupled-herbs on coronary heart disease. PMID:31852981
Drug repurposing to improve treatment of rheumatic autoimmune inflammatory diseases. PMID:31831878
Diphenyl Ditelluride: Redox-Modulating and Antiproliferative Properties. PMID:31772702
Computational/in silico methods in drug target and lead prediction. PMID:31711157
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
Network inference with ensembles of bi-clustering trees. PMID:31660848
Evaluation of the target genes of arsenic trioxide in pancreatic cancer by bioinformatics analysis. PMID:31612027
Comprehensive investigation of the clinical significance and molecular mechanisms of plasmacytoma variant translocation 1 in sarcoma using genome-wide RNA sequencing data. PMID:31598169
Erxian Decoction Attenuates TNF-α Induced Osteoblast Apoptosis by Modulating the Akt/Nrf2/HO-1 Signaling Pathway. PMID:31551787
Drug repurposing for breast cancer therapy: Old weapon for new battle. PMID:31550502
The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology. PMID:31412658
Metabolomic characterization of myocardial ischemia-reperfusion injury in ST-segment elevation myocardial infarction patients undergoing percutaneous coronary intervention. PMID:31409856
Identify the Key Active Ingredients and Pharmacological Mechanisms of Compound XiongShao Capsule in Treating Diabetic Peripheral Neuropathy by Network Pharmacology Approach. PMID:31210774
Pathway Interactions Based on Drug-Induced Datasets. PMID:31205412
Control of multilayer biological networks and applied to target identification of complex diseases. PMID:31138124
Epigenetic Modulators as Potential Multi-targeted Drugs Against Hedgehog Pathway for Treatment of Cancer. PMID:30993446
Systematically Characterize the Anti-Alzheimer's Disease Mechanism of Lignans from S. chinensis based on In-Vivo Ingredient Analysis and Target-Network Pharmacology Strategy by UHPLC⁻Q-TOF-MS. PMID:30934777
Genome-scale integrated analysis to identify prospective molecular mechanisms and therapeutic targets in isocitrate dehydrogenase 2 R140Q-mutated acute myeloid leukemia. PMID:30896832
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. PMID:30768156
Context-sensitive network analysis identifies food metabolites associated with Alzheimer's disease: an exploratory study. PMID:30704467
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. PMID:30679503
Resveratrol and Its Human Metabolites-Effects on Metabolic Health and Obesity. PMID:30641865
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing. PMID:30624606
An integrative machine learning approach for prediction of toxicity-related drug safety. PMID:30515477
Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs. PMID:30410047
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. PMID:30407536
Differentially expressed protein and gene analysis revealed the effects of temperature on changes in ascorbic acid metabolism in harvested tea leaves. PMID:30302261
Imatinib inhibits CSF1R that stimulates proliferation of rheumatoid arthritis fibroblast-like synoviocytes. PMID:30281780
Tumor-preventing activity of aspirin in multiple cancers based on bioinformatic analyses. PMID:30280037
An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example. PMID:30189851
A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project. PMID:30094994
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
In silico approach in reveal traditional medicine plants pharmacological material basis. PMID:29946351
DPubChem: a web tool for QSAR modeling and high-throughput virtual screening. PMID:29904147
Identification of Steroidogenic Components Derived From Gardenia jasminoides Ellis Potentially Useful for Treating Postmenopausal Syndrome. PMID:29899696
Changing Trends in Computational Drug Repositioning. PMID:29874824
Heterogeneous network propagation for herb target identification. PMID:29589568
Impact of Aspirin Eugenol Ester on Cyclooxygenase-1, Cyclooxygenase-2, C-Reactive Protein, Prothrombin and Arachidonate 5-Lipoxygenase in Healthy Rats. PMID:29552053
New evidence of connections between increased O-GlcNAcylation and inflammasome in the oral mucosa of patients with oral lichen planus. PMID:29247492
Identifying relationships between unrelated pharmaceutical target proteins on the basis of shared active compounds. PMID:28884009
GYY4137, a Hydrogen Sulfide Donor Modulates miR194-Dependent Collagen Realignment in Diabetic Kidney. PMID:28883608
Benzo[a]pyrene-induced metabolic shift from glycolysis to pentose phosphate pathway in the human bladder cancer cell line RT4. PMID:28851999
Integrative network and transcriptomics-based approach predicts genotype- specific drug combinations for melanoma. PMID:28815138
Using Coexpression Protein Interaction Network Analysis to Identify Mechanisms of Danshensu Affecting Patients with Coronary Heart Disease. PMID:28629174
Predicting anatomic therapeutic chemical classification codes using tiered learning. PMID:28617230
TCM-Mesh: The database and analytical system for network pharmacology analysis for TCM preparations. PMID:28588237
Postzygotic single-nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations. PMID:28503910
Personalizing Chinese medicine by integrating molecular features of diseases and herb ingredient information: application to acute myeloid leukemia. PMID:28454110
Network-based analysis of transcriptional profiles from chemical perturbations experiments. PMID:28361664
A network-based method for mechanistic investigation of Shexiang Baoxin Pill's treatment of cardiovascular diseases. PMID:28272527
Data-Driven Prediction of Beneficial Drug Combinations in Spontaneous Reporting Systems. PMID:28269877
A Systematic Framework for Drug Repositioning from Integrated Omics and Drug Phenotype Profiles Using Pathway-Drug Network. PMID:28127549
Computational polypharmacology: a new paradigm for drug discovery. PMID:28067061
DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning. PMID:27895719
DPDR-CPI, a server that predicts Drug Positioning and Drug Repositioning via Chemical-Protein Interactome. PMID:27805045
The Use of Gene Ontology Term and KEGG Pathway Enrichment for Analysis of Drug Half-Life. PMID:27780226
To Unveil the Molecular Mechanisms of Qi and Blood through Systems Biology-Based Investigation into Si-Jun-Zi-Tang and Si-Wu-Tang formulae. PMID:27677604
A corpus for plant-chemical relationships in the biomedical domain. PMID:27650402
Identification of biomarkers for periodontal disease using the immunoproteomics approach. PMID:27635317
DNA microarray of global transcription factor mutant reveals membrane-related proteins involved in n-butanol tolerance in Escherichia coli. PMID:27252779
Host, pathogen and environment: a bacterial gbpA gene expression study in response to magnesium environment and presence of prawn carapace and commercial chitin. PMID:27231485
Enzymatic Antioxidant Systems in Early Anaerobes: Theoretical Considerations. PMID:27176812
Metabolomic network analysis of estrogen-stimulated MCF-7 cells: a comparison of overrepresentation analysis, quantitative enrichment analysis and pathway analysis versus metabolite network analysis. PMID:27039105
HerDing: herb recommendation system to treat diseases using genes and chemicals. PMID:26980517
Deciphering the Potential Pharmaceutical Mechanism of Chinese Traditional Medicine (Gui-Zhi-Shao-Yao-Zhi-Mu) on Rheumatoid Arthritis. PMID:26935797
BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. PMID:26879404
Prediction of disease-gene-drug relationships following a differential network analysis. PMID:26775695
Mining Chemical Activity Status from High-Throughput Screening Assays. PMID:26658480
A Systems Biology-Based Investigation into the Pharmacological Mechanisms of Sheng-ma-bie-jia-tang Acting on Systemic Lupus Erythematosus by Multi-Level Data Integration. PMID:26560501
Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach. PMID:26504486
Mechanism of Cisplatin-Induced Cytotoxicity Is Correlated to Impaired Metabolism Due to Mitochondrial ROS Generation. PMID:26247588
A Method to Combine Signals from Spontaneous Reporting Systems and Observational Healthcare Data to Detect Adverse Drug Reactions. PMID:26153397
Many InChIs and quite some feat. PMID:26081259
Identification of New Candidate Genes and Chemicals Related to Esophageal Cancer Using a Hybrid Interaction Network of Chemicals and Proteins. PMID:26058041
An Ebola virus-centered knowledge base. PMID:26055098
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. PMID:26050742
The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer. PMID:26047514
Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System. PMID:25951454
GraphSAW: a web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data. PMID:25881043
Identification of novel thyroid cancer-related genes and chemicals using shortest path algorithm. PMID:25874234
Prediction of drug indications based on chemical interactions and chemical similarities. PMID:25821813
Proteomic analysis and identification of cellular interactors of the giant ubiquitin ligase HERC2. PMID:25476789
Exploring the ligand-protein networks in traditional chinese medicine: current databases, methods and applications. PMID:25387968
Finding candidate drugs for hepatitis C based on chemical-chemical and chemical-protein interactions. PMID:25225900
Drug repositioning discovery for early- and late-stage non-small-cell lung cancer. PMID:25210704
Curation and analysis of multitargeting agents for polypharmacological modeling. PMID:25133604
An inverse small molecule screen to design a chemically defined medium supporting long-term growth of Drosophila cell lines. PMID:25096480
PPI layouts: BioJS components for the display of Protein-Protein Interactions. PMID:25075288
In silico identification of potential targets and drugs for non-small cell lung cancer. PMID:25014226
Pregnancy-induced gingivitis and OMICS in dentistry: in silico modeling and in vivo prospective validation of estradiol-modulated inflammatory biomarkers. PMID:24983467
A web-based protein interaction network visualizer. PMID:24885165
DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. PMID:24875476
Prediction of cancer drugs by chemical-chemical interactions. PMID:24498372
dTGS: Method for Effective Components Identification from Traditional Chinese Medicine Formula and Mechanism Analysis. PMID:24454516
Prediction of drugs target groups based on ChEBI ontology. PMID:24350241
Combining heterogenous data for prediction of disease related and pharmacogenes. PMID:24297559
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Integrating in silico resources to map a signaling network. PMID:24233784
Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways. PMID:24083237
Predicting drugs side effects based on chemical-chemical interactions and protein-chemical interactions. PMID:24078917
Computational methods for drug design and discovery: focus on China. PMID:24035675
Discovery of a kernel for controlling biomolecular regulatory networks. PMID:23860463
Exploring the ligand-protein networks in traditional chinese medicine: current databases, methods, and applications. PMID:23818932
Major components of energy drinks (caffeine, taurine, and guarana) exert cytotoxic effects on human neuronal SH-SY5Y cells by decreasing reactive oxygen species production. PMID:23766861
Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network. PMID:23762317
Systematic prediction of pharmacodynamic drug-drug interactions through protein-protein-interaction network. PMID:23555229
Predicting chemical toxicity effects based on chemical-chemical interactions. PMID:23457578
Exploring the multifactorial nature of autism through computational systems biology: calcium and the Rho GTPase RAC1 under the spotlight. PMID:23456597
Visualization of protein interaction networks: problems and solutions. PMID:23368786
Polypharmacology: drug discovery for the future. PMID:23272792
TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. PMID:23203875
Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins. PMID:23029334
ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. PMID:22962483
Mining the pharmacogenomics literature--a survey of the state of the art. PMID:22833496
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
Gastrin-releasing peptide receptor antagonism induces protection from lethal sepsis: involvement of toll-like receptor 4 signaling. PMID:22735756
Applications of natural language processing in biodiversity science. PMID:22685456
Possible links between sickle cell crisis and pentavalent antimony. PMID:22665619
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. PMID:22609849
iFad: an integrative factor analysis model for drug-pathway association inference. PMID:22581178
Chemocentric informatics approach to drug discovery: identification and experimental validation of selective estrogen receptor modulators as ligands of 5-hydroxytryptamine-6 receptors and as potential cognition enhancers. PMID:22537153
Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities. PMID:22514724
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
IMID: integrated molecular interaction database. PMID:22238258
Predicting biological functions of compounds based on chemical-chemical interactions. PMID:22220213
Genome-environment interactions that modulate aging: powerful targets for drug discovery. PMID:22090473
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
Epigenetics in traditional chinese pharmacy: a bioinformatic study at pharmacopoeia scale. PMID:21785634
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. PMID:21676938
Preferential regulation of miRNA targets by environmental chemicals in the human genome. PMID:21592377
ChemMine tools: an online service for analyzing and clustering small molecules. PMID:21576229
Linked open drug data for pharmaceutical research and development. PMID:21575203
Discovering the targets of drugs via computational systems biology. PMID:21566122
Integrative computational protocol for the discovery of inhibitors of the Helicobacter pylori nickel response regulator (NikR). PMID:21360181
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. PMID:21119626
Recent progress in automatically extracting information from the pharmacogenomic literature. PMID:21047206
Molecular networks in drug discovery. PMID:20932236
The Comparative Toxicogenomics Database: update 2011. PMID:20864448
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. PMID:20727200
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. PMID:20689020
Publishing Chinese medicine knowledge as Linked Data on the Web. PMID:20663193
Complexomics study of two Helicobacter pylori strains of two pathological origins: potential targets for vaccine development and new insight in bacteria metabolism. PMID:20610778
BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects. PMID:20576702
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. PMID:20513238
Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. PMID:20434586
Teaching computers to read the pharmacogenomics literature ... so you don't have to. PMID:20350132
Mining connections between chemicals, proteins, and diseases extracted from Medline annotations. PMID:20348023
Visualization of macromolecular structures. PMID:20195256
iPHACE: integrative navigation in pharmacological space. PMID:20156991
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
STITCH 2: an interaction network database for small molecules and proteins. PMID:19897548
T3DB: a comprehensively annotated database of common toxins and their targets. PMID:19897546
Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling. PMID:19825513
Predicting drug side-effects by chemical systems biology. PMID:19723347
Automatic parameter learning for multiple local network alignment. PMID:19645599
Reflect: augmented browsing for the life scientist. PMID:19513049
Bruton's tyrosine kinase revealed as a negative regulator of Wnt-beta-catenin signaling. PMID:19471023
jClust: a clustering and visualization toolbox. PMID:19454618
Linking fold, function and phylogeny: a comparative genomics view on protein (domain) evolution. PMID:19440449
Generating genome-scale candidate gene lists for pharmacogenomics. PMID:19369935
OnTheFly: a tool for automated document-based text annotation, data linking and network generation. PMID:19223449
Prediction of interaction between small molecule and enzyme using AdaBoost. PMID:19219560
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. PMID:19054114
A survey of visualization tools for biological network analysis. PMID:19040716
Chemical databases for environmental health and clinical research. PMID:18996453
Update of KDBI: Kinetic Data of Bio-molecular Interaction database. PMID:18971255
STRING 8--a global view on proteins and their functional interactions in 630 organisms. PMID:18940858
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. PMID:18782832
The Molecular Biology Database Collection: 2008 update. PMID:18025043
STITCH 4: integration of protein-chemical interactions with user data PubMed citations: 170.

170 articles citing: STITCH 4: integration of protein-chemical interactions with user data

Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Berberine in the Treatment of Ischaemic Stroke. PMID:35815278
SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19. PMID:35784208
Discovery of new drug indications for COVID-19: A drug repurposing approach. PMID:35609015
Drug-Drug Interactions Prediction Using Fingerprint Only. PMID:35586666
Deciphering the Underlying Mechanisms of Formula Le-Cao-Shi Against Liver Injuries by Integrating Network Pharmacology, Metabonomics, and Experimental Validation. PMID:35548342
Similarity-Based Method with Multiple-Feature Sampling for Predicting Drug Side Effects. PMID:35401786
Computational Methods for Drug Repurposing. PMID:35230686
The Neuroprotective Effects of Coreopsis tinctoria and Its Mechanism: Interpretation of Network Pharmacological and Experimental Data. PMID:35222009
Network Pharmacology Study on Molecular Mechanisms of Zhishi Xiebai Guizhi Decoction in the Treatment of Coronary Heart Disease. PMID:34966435
Artificial intelligence in clinical research of cancers. PMID:34929741
Small molecules for cell reprogramming: a systems biology analysis. PMID:34919532
Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on "drug-target-pathway" heterogenous network. PMID:34544480
Genetic Polymorphisms of Pesticide-Metabolizing Enzymes and Transporters in Agricultural Workers and Thyroid Hormone Levels. PMID:34434063
Role of MT1A Polymorphism and Environmental Mercury Exposure on the Montreal Cognitive Assessment (MoCA). PMID:34326641
Baicalin Rescues Cognitive Dysfunction, Mitigates Neurodegeneration, and Exerts Anti-Epileptic Effects Through Activating TLR4/MYD88/Caspase-3 Pathway in Rats. PMID:34321866
In silico drug repositioning using deep learning and comprehensive similarity measures. PMID:34074242
Adenosine and Cordycepin Accelerate Tissue Remodeling Process through Adenosine Receptor Mediated Wnt/β-Catenin Pathway Stimulation by Regulating GSK3b Activity. PMID:34070360
The Involvement of Selenium in Type 2 Diabetes Development Related to Obesity and Low Grade Inflammation. PMID:33883916
Expression level of long non-coding RNA colon adenocarcinoma hypermethylated serves as a novel prognostic biomarker in patients with thyroid carcinoma. PMID:33792624
The Advantages of Connectivity Map Applied in Traditional Chinese Medicine. PMID:33776757
UXT antisense RNA 1 sever as a novel prognostic long non-coding RNA in early stage pancreatic ductal adenocarcinoma patients after receiving pancreaticoduodenectomy. PMID:33754011
Network Pharmacological Study of Achyranthis bidentatae Radix Effect on Bone Trauma. PMID:33748269
Novel Computational Approach to Predict Off-Target Interactions for Small Molecules. PMID:33693348
A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds. PMID:33519445
iMPTCE-Hnetwork: A Multilabel Classifier for Identifying Metabolic Pathway Types of Chemicals and Enzymes with a Heterogeneous Network. PMID:33488764
Exploring the Mechanism of Gyejibokryeong-hwan against Atherosclerosis Using Network Pharmacology and Molecular Docking. PMID:33321972
Interleukin 25 (IL-25) expression in cholangiocarcinoma. PMID:33163180
Uncovering the Mechanisms of Cryptotanshinone as a Therapeutic Agent Against Hepatocellular Carcinoma. PMID:32903546
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
Decoding altitude-activated regulatory mechanisms occurring during apple peel ripening. PMID:32821403
Identification of potential prognostic small nucleolar RNA biomarkers for predicting overall survival in patients with sarcoma. PMID:32780509
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
Medicinal Properties of Lilium candidum L. and Its Phytochemicals. PMID:32751398
Prediction of Drug Side Effects with a Refined Negative Sample Selection Strategy. PMID:32454877
In silico analysis of functional linkage among arsenic induced MATE genes in rice. PMID:32435604
A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches. PMID:32322011
Mechanism of tanshinones and phenolic acids from Danshen in the treatment of coronary heart disease based on co-expression network. PMID:32020855
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Drug-target interaction prediction using Multi Graph Regularized Nuclear Norm Minimization. PMID:31945078
Serum coiled-coil domain containing 25 protein as a potential screening/diagnostic biomarker for cholangiocarcinoma. PMID:31897206
An Insight Into the Molecular Mechanism of Berberine Towards Multiple Cancer Types Through Systems Pharmacology. PMID:31447670
Network Pharmacology-Based Prediction and Verification of the Targets and Mechanism for Panax Notoginseng Saponins against Coronary Heart Disease. PMID:31354855
Uncovering the Pharmacological Mechanism of Chaibei Zhixian Decoction on Epilepsy by Network Pharmacology Analysis. PMID:31214268
L2,1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions. PMID:31182006
Auto-Generated Physiological Chain Data for an Ontological Framework for Pharmacology and Mechanism of Action to Determine Suspected Drugs in Cases of Dysuria. PMID:31119651
Identification of pathways associated with chemosensitivity through network embedding. PMID:30893303
Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment. PMID:30846939
Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes. PMID:30820351
Network Pharmacology Integrated Molecular Docking Reveals the Antiosteosarcoma Mechanism of Biochanin A. PMID:30723510
Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data. PMID:30717646
The computational prediction of drug-disease interactions using the dual-network L2,1-CMF method. PMID:30611214
MDAD: A Special Resource for Microbe-Drug Associations. PMID:30581775
Transcriptomic profiles of muscle, heart, and spleen in reaction to circadian heat stress in Ethiopian highland and lowland male chicken. PMID:30565091
A Network Pharmacology Approach to Uncover the Mechanisms of Shen-Qi-Di-Huang Decoction against Diabetic Nephropathy. PMID:30519269
Discovering proteins for chemoprevention and chemotherapy by curcumin in liver fluke infection-induced bile duct cancer. PMID:30440021
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. PMID:30285109
Context-dependent prediction of protein complexes by SiComPre. PMID:30245847
Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers. PMID:30123424
Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence. PMID:30096807
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
Phenotype-oriented network analysis for discovering pharmacological effects of natural compounds. PMID:30076354
Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings. PMID:30010749
Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis. PMID:29943236
DPubChem: a web tool for QSAR modeling and high-throughput virtual screening. PMID:29904147
Combining mechanism-based prediction with patient-based profiling for psoriasis metabolomics biomarker discovery. PMID:29854244
Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error. PMID:29808027
Community-driven roadmap for integrated disease maps. PMID:29688273
A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer. PMID:29670137
Extensive impact of non-antibiotic drugs on human gut bacteria. PMID:29555994
Oasis 2: improved online analysis of small RNA-seq data. PMID:29444641
In silico profiling of systemic effects of drugs to predict unexpected interactions. PMID:29371651
Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. PMID:29344883
The role of NFκB in spheroid formation of human breast cancer cells cultured on the Random Positioning Machine. PMID:29343717
EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer. PMID:29228577
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. PMID:29170530
Evidence-Based Precision Oncology with the Cancer Targetome. PMID:28964549
Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy. PMID:28956927
In Silico Prediction of the Anti-Depression Mechanism of a Herbal Formula (Tiansi Liquid) Containing Morinda officinalis and Cuscuta chinensis. PMID:28954415
Large-scale cross-species chemogenomic platform proposes a new drug discovery strategy of veterinary drug from herbal medicines. PMID:28915268
From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns. PMID:28900272
A computational method for the identification of candidate drugs for non-small cell lung cancer. PMID:28820893
Screening drug-target interactions with positive-unlabeled learning. PMID:28808275
High expression of CCDC25 in cholangiocarcinoma tissue samples. PMID:28789463
Machine learning for predicting lifespan-extending chemical compounds. PMID:28783712
Metabolome alterations in severe critical illness and vitamin D status. PMID:28750641
Acute coronary syndrome and acute kidney injury: role of inflammation in worsening renal function. PMID:28747177
Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli. PMID:28727780
Using Coexpression Protein Interaction Network Analysis to Identify Mechanisms of Danshensu Affecting Patients with Coronary Heart Disease. PMID:28629174
Contextualization of drug-mediator relations using evidence networks. PMID:28617226
MetabolitePredict: A de novo human metabolomics prediction system and its applications in rheumatoid arthritis. PMID:28600026
Data-driven prediction of adverse drug reactions induced by drug-drug interactions. PMID:28595649
TCM-Mesh: The database and analytical system for network pharmacology analysis for TCM preparations. PMID:28588237
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. PMID:28577120
Network-assisted target identification for haploinsufficiency and homozygous profiling screens. PMID:28574983
Bactericidal potential of silver nanoparticles synthesized using cell-free extract of Comamonas acidovorans: in vitro and in silico approaches. PMID:28555428
AlzhCPI: A knowledge base for predicting chemical-protein interactions towards Alzheimer's disease. PMID:28542505
Bioinformatics and in vitro experimental analyses identify the selective therapeutic potential of interferon gamma and apigenin against cervical squamous cell carcinoma and adenocarcinoma. PMID:28526810
Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure. PMID:28341699
Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes. PMID:28294568
Variability in statin-induced changes in gene expression profiles of pancreatic cancer. PMID:28276528
Pharmacoinformatics, Adaptive Evolution, and Elucidation of Six Novel Compounds for Schizophrenia Treatment by Targeting DAOA (G72) Isoforms. PMID:28197415
Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks. PMID:28155715
Drug-target interaction prediction via class imbalance-aware ensemble learning. PMID:28155697
Predictive characterization of hypothetical proteins in Staphylococcus aureus NCTC 8325. PMID:28149057
A Systematic Framework for Drug Repositioning from Integrated Omics and Drug Phenotype Profiles Using Pathway-Drug Network. PMID:28127549
Combining Chemical Profiling and Network Analysis to Investigate the Pharmacology of Complex Prescriptions in Traditional Chinese Medicine. PMID:28084407
Computational polypharmacology: a new paradigm for drug discovery. PMID:28067061
Open Targets: a platform for therapeutic target identification and validation. PMID:27899665
DIFFERENTIAL PATHWAY DEPENDENCY DISCOVERY ASSOCIATED WITH DRUG RESPONSE ACROSS CANCER CELL LINES. PMID:27897001
DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning. PMID:27895719
Alpha-enolase on apical surface of renal tubular epithelial cells serves as a calcium oxalate crystal receptor. PMID:27796334
PubMedPortable: A Framework for Supporting the Development of Text Mining Applications. PMID:27706202
Drug repurposing for glioblastoma based on molecular subtypes. PMID:27697594
Towards understanding brain-gut-microbiome connections in Alzheimer's disease. PMID:27585440
High expression of apoptosis-inducing factor, mitochondrion-associated 3 (AIFM3) in human cholangiocarcinoma. PMID:27473083
Metabolites Associated With Malnutrition in the Intensive Care Unit Are Also Associated With 28-Day Mortality. PMID:27406941
A synopsis on aging-Theories, mechanisms and future prospects. PMID:27353257
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. PMID:27330567
Comprehensive analysis of high-throughput screens with HiTSeekR. PMID:27330136
CART-a chemical annotation retrieval toolkit. PMID:27256313
WAX INDUCER1 (HvWIN1) transcription factor regulates free fatty acid biosynthetic genes to reinforce cuticle to resist Fusarium head blight in barley spikelets. PMID:27194736
Inferring gene targets of drugs and chemical compounds from gene expression profiles. PMID:27153589
Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network. PMID:27149165
A Drug-Centric View of Drug Development: How Drugs Spread from Disease to Disease. PMID:27124390
A Network Pharmacology Approach to Uncover the Pharmacological Mechanism of XuanHuSuo Powder on Osteoarthritis. PMID:27110264
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PMID:27096930
Significant Modules and Biological Processes between Active Components of Salvia miltiorrhiza Depside Salt and Aspirin. PMID:27069488
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. PMID:27055828
Systematic discovery of drug action mechanisms by an integrated chemical genomics approach: identification of functional disparities between azacytidine and decitabine. PMID:27036028
ITPI: Initial Transcription Process-Based Identification Method of Bioactive Components in Traditional Chinese Medicine Formula. PMID:27034696
Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform. PMID:27013226
Novel loci and pathways significantly associated with longevity. PMID:26912274
ChemProt-3.0: a global chemical biology diseases mapping. PMID:26876982
Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7. PMID:26858419
The exploration of network motifs as potential drug targets from post-translational regulatory networks. PMID:26853265
Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis. PMID:26713275
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. PMID:26590256
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PMID:26555441
Potential Compounds for Oral Cancer Treatment: Resveratrol, Nimbolide, Lovastatin, Bortezomib, Vorinostat, Berberine, Pterostilbene, Deguelin, Andrographolide, and Colchicine. PMID:26536350
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations. PMID:26492574
The SIDER database of drugs and side effects. PMID:26481350
From drug response profiling to target addiction scoring in cancer cell models. PMID:26438695
The Mechanism Research of Qishen Yiqi Formula by Module-Network Analysis. PMID:26379745
Network pharmacological identification of active compounds and potential actions of Erxian decoction in alleviating menopause-related symptoms. PMID:26191080
SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. PMID:26130660
A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat. PMID:26100814
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PMID:26083494
Many InChIs and quite some feat. PMID:26081259
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. PMID:26078786
Improving compound-protein interaction prediction by building up highly credible negative samples. PMID:26072486
A survey on the computational approaches to identify drug targets in the postgenomic era. PMID:26060814
Comprehensive prediction of drug-protein interactions and side effects for the human proteome. PMID:26057345
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. PMID:26050742
The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer. PMID:26047514
Enriched transcription factor signatures in triple negative breast cancer indicates possible targeted therapies with existing drugs. PMID:26005638
Oasis: online analysis of small RNA deep sequencing data. PMID:25701573
MMP-9- and NMDA receptor-mediated mechanism of diabetic renovascular remodeling and kidney dysfunction: hydrogen sulfide is a key modulator. PMID:25659756
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
Cellular manganese content is developmentally regulated in human dopaminergic neurons. PMID:25348053
A gene expression signature-based approach reveals the mechanisms of action of the Chinese herbal medicine berberine. PMID:25227736
BalestraWeb: efficient online evaluation of drug-target interactions. PMID:25192741
Computational methods for analysis and inference of kinase/inhibitor relationships. PMID:25071826
TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants. PMID:24930145
Shotgun proteomics analysis of proliferating STRO-1-positive human dental pulp cell after exposure to nacreous water-soluble matrix. PMID:24923583
STITCH 3: zooming in on protein-chemical interactions PubMed citations: 122.

122 articles citing: STITCH 3: zooming in on protein-chemical interactions

Predicting protein network topology clusters from chemical structure using deep learning. PMID:35841114
Identifying the molecular targets of Salvia miltiorrhiza (SM) in ox-LDL induced macrophage-derived foam cells based on the integration of metabolomics and network pharmacology. PMID:35542903
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PMID:35402106
Investigation of Roles of TaTALE Genes during Development and Stress Response in Bread Wheat. PMID:35270056
Computational Methods for Drug Repurposing. PMID:35230686
Interactome of Arabidopsis Thaliana. PMID:35161331
Wenxin Keli for the Treatment of Arrhythmia-Systems Pharmacology and In Vivo Pharmacological Assessment. PMID:34512338
Network Pharmacology-Based Mechanistic Investigation of Jinshui Huanxian Formula Acting on Idiopathic Pulmonary Fibrosis. PMID:34306156
The Clinical Efficiency and the Mechanism of Sanzi Yangqin Decoction for Chronic Obstructive Pulmonary Disease. PMID:34221077
Study on the Mechanism of the Danggui-Chuanxiong Herb Pair on Treating Thrombus through Network Pharmacology and Zebrafish Models. PMID:34124490
Deep learning integration of molecular and interactome data for protein-compound interaction prediction. PMID:33933121
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
Application and evaluation of knowledge graph embeddings in biomedical data. PMID:33816992
Robustness and lethality in multilayer biological molecular networks. PMID:33247151
CGINet: graph convolutional network-based model for identifying chemical-gene interaction in an integrated multi-relational graph. PMID:33243142
Anti-inflammatory activity of Radix Angelicae biseratae in the treatment of osteoarthritis determined by systematic pharmacology and in vitro experiments. PMID:33235614
Network Pharmacology Combined with Transcriptional Analysis to Unveil the Biological Basis of Astaxanthin in Reducing the Oxidative Stress Induced by Diabetes Mellitus. PMID:33204134
A Systematic Pharmacology and In Vitro Study to Identify the Role of the Active Compounds of Achyranthes bidentata in the Treatment of Osteoarthritis. PMID:32925869
Enhancing and Complementary Mechanisms of Synergistic Action of Acori Tatarinowii Rhizoma and Codonopsis Radix for Alzheimer's Disease Based on Systems Pharmacology. PMID:32802132
Identification of potential prognostic small nucleolar RNA biomarkers for predicting overall survival in patients with sarcoma. PMID:32780509
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
Ingredients, Anti-Liver Cancer Effects and the Possible Mechanism of DWYG Formula Based on Network Prediction. PMID:32523357
An Integrated Pharmacology-Based Analysis for Antidepressant Mechanism of Chinese Herbal Formula Xiao-Yao-San. PMID:32256358
Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis. PMID:32063919
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
A Network Pharmacology Approach to Reveal the Underlying Mechanisms of Paeonia lactiflora Pall. On the Treatment of Alzheimer's Disease. PMID:31827565
Systematic Elucidation of the Mechanism of Genistein against Pulmonary Hypertension via Network Pharmacology Approach. PMID:31703458
Drug repurposing for breast cancer therapy: Old weapon for new battle. PMID:31550502
Network Pharmacology Identifies the Mechanisms of Action of Shaoyao Gancao Decoction in the Treatment of Osteoarthritis. PMID:31409761
Revealing Drug-Target Interactions with Computational Models and Algorithms. PMID:31052598
Effects and possible mechanism of Ruyiping formula application to breast cancer based on network prediction. PMID:30918282
Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction. PMID:30768150
Novel mutation G324C in WNT1 mapped in a large Pakistani family with severe recessively inherited Osteogenesis Imperfecta. PMID:30447692
Systems biology-based drug repositioning identifies digoxin as a potential therapy for groups 3 and 4 medulloblastoma. PMID:30355798
Deep learning-based transcriptome data classification for drug-target interaction prediction. PMID:30255785
A network pharmacology approach to explore the mechanisms of Erxian decoction in polycystic ovary syndrome. PMID:30181771
DeCoST: A New Approach in Drug Repurposing From Control System Theory. PMID:29922160
Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions. PMID:29876834
Systematic Identification of Druggable Epithelial-Stromal Crosstalk Signaling Networks in Ovarian Cancer. PMID:29860390
Integrated Metabolomics and Network Pharmacology Approach to Explain Possible Action Mechanisms of Xin-Sheng-Hua Granule for Treating Anemia. PMID:29551975
Identification and in silico characterization of a novel p.P208PfsX1 mutation in V-ATPase a3 subunit associated with autosomal recessive osteopetrosis in a Pakistani family. PMID:29237407
Target-similarity search using Plasmodium falciparum proteome identifies approved drugs with anti-malarial activity and their possible targets. PMID:29088219
System Pharmacology-Based Dissection of the Synergistic Mechanism of Huangqi and Huanglian for Diabetes Mellitus. PMID:29051733
Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery. PMID:28983419
Identifying relationships between unrelated pharmaceutical target proteins on the basis of shared active compounds. PMID:28884009
Discovery of novel therapeutic properties of drugs from transcriptional responses based on multi-label classification. PMID:28769090
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
Herb pair Danggui-Honghua: mechanisms underlying blood stasis syndrome by system pharmacology approach. PMID:28074863
Prior knowledge-based approach for associating contaminants with biological effects: A case study in the St. Croix River basin, MN, WI, USA. PMID:27939634
Biomolecular Network-Based Synergistic Drug Combination Discovery. PMID:27891522
Systems pharmacology exploration of botanic drug pairs reveals the mechanism for treating different diseases. PMID:27841365
A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects. PMID:27673331
StemCellCKB: An Integrated Stem Cell-Specific Chemogenomics KnowledgeBase for Target Identification and Systems-Pharmacology Research. PMID:27643925
Knowledge Discovery from Biomedical Ontologies in Cross Domains. PMID:27548262
Host, pathogen and the environment: the case of Macrobrachium rosenbergii, Vibrio parahaemolyticus and magnesium. PMID:27114742
Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state. PMID:26871731
COLLECTIVE PAIRWISE CLASSIFICATION FOR MULTI-WAY ANALYSIS OF DISEASE AND DRUG DATA. PMID:26776175
A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans. PMID:26676933
Drug target prioritization by perturbed gene expression and network information. PMID:26615774
Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. PMID:26573537
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks. PMID:26469276
DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. PMID:26423722
A Rich-Club Organization in Brain Ischemia Protein Interaction Network. PMID:26310627
Mechanism of Cisplatin-Induced Cytotoxicity Is Correlated to Impaired Metabolism Due to Mitochondrial ROS Generation. PMID:26247588
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Many InChIs and quite some feat. PMID:26081259
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. PMID:26078786
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. PMID:26050742
A Network-Based Target Overlap Score for Characterizing Drug Combinations: High Correlation with Cancer Clinical Trial Results. PMID:26047322
Gene Expression Profiling and Pathway Network Analysis Predicts a Novel Antitumor Function for a Botanical-Derived Drug, PG2. PMID:25972907
Protective effect of Daming capsule against chronic cerebral ischemia. PMID:25966684
Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature. PMID:25860223
Molecular handoffs in nitrergic neurotransmission. PMID:25705621
In silico repositioning-chemogenomics strategy identifies new drugs with potential activity against multiple life stages of Schistosoma mansoni. PMID:25569258
Analysis of individual protein regions provides novel insights on cancer pharmacogenomics. PMID:25568936
Systematic prediction of drug combinations based on clinical side-effects. PMID:25418113
Text mining in cancer gene and pathway prioritization. PMID:25392685
Proteomics for systems toxicology. PMID:25379146
A novel systems pharmacology model for herbal medicine injection: a case using Reduning injection. PMID:25366653
Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level. PMID:25313158
Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs. PMID:25276232
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. PMID:25165489
An inverse small molecule screen to design a chemically defined medium supporting long-term growth of Drosophila cell lines. PMID:25096480
Systems pharmacology dissection of multi-scale mechanisms of action for herbal medicines in stroke treatment and prevention. PMID:25093322
MPINet: metabolite pathway identification via coupling of global metabolite network structure and metabolomic profile. PMID:25057481
Exploiting large-scale drug-protein interaction information for computational drug repurposing. PMID:24950817
DrugComboRanker: drug combination discovery based on target network analysis. PMID:24931988
Targeting molecular networks for drug research. PMID:24926314
A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α1-antitrypsin deficiency. PMID:24838285
The use of functional chemical-protein associations to identify multi-pathway renoprotectants. PMID:24830678
Fetal alcohol syndrome, chemo-biology and OMICS: ethanol effects on vitamin metabolism during neurodevelopment as measured by systems biology analysis. PMID:24816220
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation. PMID:24565337
Visualization of network target crosstalk optimizes drug synergism in myocardial ischemia. PMID:24505402
Novel factors in the pathogenesis of psoriasis and potential drug candidates are found with systems biology approach. PMID:24303025
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Predicting drug-target interactions using probabilistic matrix factorization. PMID:24289468
Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. PMID:24239728
CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction. PMID:24206562
Mouse model phenotypes provide information about human drug targets. PMID:24158600
DGIdb: mining the druggable genome. PMID:24122041
Computational methods for drug design and discovery: focus on China. PMID:24035675
Navigating traditional chinese medicine network pharmacology and computational tools. PMID:23983798
Venus Flytrap (Dionaea muscipula Solander ex Ellis) Contains Powerful Compounds that Prevent and Cure Cancer. PMID:23971004
Automated QuantMap for rapid quantitative molecular network topology analysis. PMID:23828784
Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology. PMID:23826885
Predicting drug-target interactions using restricted Boltzmann machines. PMID:23812976
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
Tumor necrosis factor receptor superfamily 10B (TNFRSF10B): an insight from structure modeling to virtual screening for designing drug against head and neck cancer. PMID:23724937
Systematic identification of proteins that elicit drug side effects. PMID:23632385
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. PMID:23632384
Clinical analysis and interpretation of cancer genome data. PMID:23589549
A systematic in silico search for target similarity identifies several approved drugs with potential activity against the Plasmodium falciparum apicoplast. PMID:23555651
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
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. PMID:23203867
The TissueNet database of human tissue protein-protein interactions. PMID:23193266
ChemProt-2.0: visual navigation in a disease chemical biology database. PMID:23185041
C²Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships. PMID:23134618
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. PMID:23118479
Gene network analysis of small molecules with autoimmune disease associated genes predicts a novel strategy for drug efficacy. PMID:23000205
STITCH 2: an interaction network database for small molecules and proteins PubMed citations: 104.

104 articles citing: STITCH 2: an interaction network database for small molecules and proteins

SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19. PMID:35784208
Discovery of new drug indications for COVID-19: A drug repurposing approach. PMID:35609015
Multi-Omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer. PMID:35574395
Investigation of the Effect of Curcumin on Protein Targets in NAFLD Using Bioinformatic Analysis. PMID:35405942
Computational Methods for Drug Repurposing. PMID:35230686
The mechanism of triptolide in the treatment of connective tissue disease-related interstitial lung disease based on network pharmacology and molecular docking. PMID:35132912
Exploring the Mechanism of Resveratrol in Reducing the Soft Tissue Damage of Osteoarthritis Based on Network Pharmacology and Experimental Pharmacology. PMID:34646331
Exploring the Pharmacological Mechanisms of Tripterygium wilfordii Hook F against Cardiovascular Disease Using Network Pharmacology and Molecular Docking. PMID:34435046
Machine learning approaches for drug combination therapies. PMID:34368832
Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome. PMID:34350693
A Combined Phytochemistry and Network Pharmacology Approach to Reveal Potential Anti-NSCLC Effective Substances and Mechanisms in Marsdenia tenacissima (Roxb.) Moon (Stem). PMID:33994999
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. PMID:33787872
A computational framework of host-based drug repositioning for broad-spectrum antivirals against RNA viruses. PMID:33665567
Global mapping of protein-metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. PMID:33568709
Network machine learning maps phytochemically rich "Hyperfoods" to fight COVID-19. PMID:33386081
Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment. PMID:33108391
signatureSearch: environment for gene expression signature searching and functional interpretation. PMID:33068417
Medicinal Properties of Lilium candidum L. and Its Phytochemicals. PMID:32751398
Applications of Network Pharmacology in Traditional Chinese Medicine Research. PMID:32148533
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Comprehensive investigation of the clinical significance and molecular mechanisms of plasmacytoma variant translocation 1 in sarcoma using genome-wide RNA sequencing data. PMID:31598169
HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods. PMID:31270435
Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. PMID:31201557
Combined metabolic, phenomic and genomic data to prioritize atrial fibrillation-related metabolites. PMID:31007735
Identification of atherosclerosis-related prioritizing metabolites based on a multi-omics composite network. PMID:30988716
Prioritization of candidate metabolites for postmenopausal osteoporosis using multi-omics composite network. PMID:30936988
Genome-scale integrated analysis to identify prospective molecular mechanisms and therapeutic targets in isocitrate dehydrogenase 2 R140Q-mutated acute myeloid leukemia. PMID:30896832
Identification of Key Metabolites for Acute Lung Injury in Patients with Sepsis. PMID:30847314
Epigallocatechin‑3‑gallate modulates long non‑coding RNA and mRNA expression profiles in lung cancer cells. PMID:30628683
Consequences of blunting the mevalonate pathway in cancer identified by a pluri-omics approach. PMID:29970880
Bioactive Nutrients and Nutrigenomics in Age-Related Diseases. PMID:28075340
Carbamate Insecticides Target Human Melatonin Receptors. PMID:28027439
Downregulation of coding transmembrane protein 35 gene inhibits cell proliferation, migration and cell cycle arrest in osteosarcoma cells. PMID:27446247
Significant Modules and Biological Processes between Active Components of Salvia miltiorrhiza Depside Salt and Aspirin. PMID:27069488
Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources. PMID:26609498
Global Prioritization of Disease Candidate Metabolites Based on a Multi-omics Composite Network. PMID:26598063
Computational and Pharmacological Target of Neurovascular Unit for Drug Design and Delivery. PMID:26579539
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. PMID:26467653
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Mechanism of Cisplatin-Induced Cytotoxicity Is Correlated to Impaired Metabolism Due to Mitochondrial ROS Generation. PMID:26247588
Label Propagation Prediction of Drug-Drug Interactions Based on Clinical Side Effects. PMID:26196247
Screening of the binding of small molecules to proteins by desorption electrospray ionization mass spectrometry combined with protein microarray. PMID:26174365
Many InChIs and quite some feat. PMID:26081259
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. PMID:26050742
Oral administration of Lactobacillus plantarum 299v modulates gene expression in the ileum of pigs: prediction of crosstalk between intestinal immune cells and sub-mucosal adipocytes. PMID:25861755
White adipose tissue reference network: a knowledge resource for exploring health-relevant relations. PMID:25466819
Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs. PMID:25276232
Profiling human protein degradome delineates cellular responses to proteasomal inhibition and reveals a feedback mechanism in regulating proteasome homeostasis. PMID:25223703
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. PMID:25204982
An inverse small molecule screen to design a chemically defined medium supporting long-term growth of Drosophila cell lines. PMID:25096480
Systematic analysis of gene properties influencing organ system phenotypes in mammalian perturbations. PMID:25061072
DINIES: drug-target interaction network inference engine based on supervised analysis. PMID:24838565
Scalable prediction of compound-protein interactions using minwise hashing. PMID:24564870
Prediction of cancer drugs by chemical-chemical interactions. PMID:24498372
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Predicting drug-target interactions using drug-drug interactions. PMID:24278248
Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network. PMID:23762317
Histone modifications and traditional Chinese medicinals. PMID:23711355
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis. PMID:23650583
Transcription networks responsible for early regulation of Salmonella-induced inflammation in the jejunum of pigs. PMID:23590759
Interaction between p53 and estradiol pathways in transcriptional responses to chemotherapeutics. PMID:23518503
Choline protects against cardiac hypertrophy induced by increased after-load. PMID:23493786
Predicting chemical toxicity effects based on chemical-chemical interactions. PMID:23457578
Comparative proteomic analysis reveals proteins putatively involved in toxin biosynthesis in the marine dinoflagellate Alexandrium catenella. PMID:23340676
Allele-specific behavior of molecular networks: understanding small-molecule drug response in yeast. PMID:23308257
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins. PMID:23029334
An overview of computational life science databases & exchange formats of relevance to chemical biology research. PMID:22934944
Identifying novel drug indications through automated reasoning. PMID:22911721
Assessing drug target association using semantic linked data. PMID:22859915
State of the art in silico tools for the study of signaling pathways in cancer. PMID:22837650
Gastrin-releasing peptide receptor antagonism induces protection from lethal sepsis: involvement of toll-like receptor 4 signaling. PMID:22735756
Behavioral barcoding in the cloud: embracing data-intensive digital phenotyping in neuropharmacology. PMID:22652049
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. PMID:22609849
Chemocentric informatics approach to drug discovery: identification and experimental validation of selective estrogen receptor modulators as ligands of 5-hydroxytryptamine-6 receptors and as potential cognition enhancers. PMID:22537153
Prediction of drug combinations by integrating molecular and pharmacological data. PMID:22219721
Network systems biology for targeted cancer therapies. PMID:22176777
ProtChemSI: a network of protein-chemical structural interactions. PMID:22110041
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
Gene expression-based chemical genomics identifies potential therapeutic drugs in hepatocellular carcinoma. PMID:22087264
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
SuperTarget goes quantitative: update on drug-target interactions. PMID:22067455
Open Babel: An open chemical toolbox. PMID:21982300
The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. PMID:21952136
Exploring pathway interactions in insulin resistant mouse liver. PMID:21843341
Linked gene networks involved in nitrogen and carbon metabolism and levels of water-soluble carbohydrate accumulation in wheat stems. PMID:21789636
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
Integrative computational biology for cancer research. PMID:21691773
Combinations of protein-chemical complex structures reveal new targets for established drugs. PMID:21573205
Using graph theory to analyze biological networks. PMID:21527005
Integrative computational protocol for the discovery of inhibitors of the Helicobacter pylori nickel response regulator (NikR). PMID:21360181
Systems biology: the next frontier for bioinformatics. PMID:21331364
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. PMID:21179023
HIT: linking herbal active ingredients to targets. PMID:21097881
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. PMID:21059682
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
Gene expression changes associated with resistance to intravenous corticosteroid therapy in children with severe ulcerative colitis. PMID:20941359
ChemProt: a disease chemical biology database. PMID:20935044
Molecular networks in drug discovery. PMID:20932236
Drug-induced regulation of target expression. PMID:20838579
Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. PMID:20572635
Visualization of omics data for systems biology. PMID:20195258
http://dx.doi.org/10.1093/nar/gkt1207

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chemical entity
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

literature curation
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: STITCH; Search Tool for Interactions of Chemicals; DOI: https://doi.org/10.25504/FAIRsharing.zhwa8x; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein-protein interactions
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

biochemical processes
metasource: re3data.org
version: re3data.org: STITCH 4.0; editing status 2020-10-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3606X last accessed: 2022-11-04

chemical models
metasource: re3data.org
version: re3data.org: STITCH 4.0; editing status 2020-10-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3606X last accessed: 2022-11-04

chemical-protein interactions
metasource: re3data.org
version: re3data.org: STITCH 4.0; editing status 2020-10-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3606X last accessed: 2022-11-04

pharmaceutical preparations
metasource: re3data.org
version: re3data.org: STITCH 4.0; editing status 2020-10-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3606X last accessed: 2022-11-04

protein interaction mapping
metasource: re3data.org
version: re3data.org: STITCH 4.0; editing status 2020-10-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3606X last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: STITCH 4.0; editing status 2020-10-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3606X last accessed: 2022-11-04

stereoisomerism
metasource: re3data.org
version: re3data.org: STITCH 4.0; editing status 2020-10-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3606X last accessed: 2022-11-04

chemistry
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

biomedical science
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.094646

chemical entity computational predictions literature curation molecular interaction protein small molecule metabolic and signaling pathways protein-protein interactions biochemical processes chemical models chemical-protein interactions pharmaceutical preparations protein interaction mapping proteins stereoisomerism chemistry biomedical science molecular interactions, pathways and networks

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DroID - Drosophila Interactions Database

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BindingDB database of measured binding affinities

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Biological General Repository for Interaction Datasets

Interologous Interaction Database

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