ArticleBioinformatics (Oxford, England)2016
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases.NPJ systems biology and applications · 2026Review
- The Human Omnibus of Targetable Pockets.Journal of cheminformatics · 2025Article
- Natural Language Processing Methods for the Study of Protein-Ligand Interactions.Journal of chemical information and modeling · 2025Review
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Article
- DiPPI: A Curated Data Set for Drug-like Molecules in Protein-Protein Interfaces.Journal of chemical information and modeling · 2024Article
- A review of deep learning methods for ligand based drug virtual screening.Fundamental research · 2024Review
- FKBP5 blockade may provide a new horizon for the treatment of stress-associated disorders: An in-silico study.Epilepsia open · 2023Article
- Databases and Tools to Investigate Protein-Metabolite Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Statistical Bioinformatics to Uncover the Underlying Biological Mechanisms That Linked Smoking with Type 2 Diabetes Patients Using Transcritpomic and GWAS Analysis.Molecules (Basel, Switzerland) · 2022Article
- Computational Methods for Drug Repurposing.Advances in experimental medicine and biology · 2022Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry.International journal of molecular sciences · 2021Review
- Machine learning approaches and databases for prediction of drug-target interaction: a survey paper.Briefings in bioinformatics · 2021Review
- Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics.Nucleic acids research · 2020Article
- Binding site matching in rational drug design: algorithms and applications.Briefings in bioinformatics · 2019Review
- Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning.Nucleic acids research · 2019Article
- Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins.Frontiers in genetics · 2019Article
- Prediction Methods of Herbal Compounds in Chinese Medicinal Herbs.Molecules (Basel, Switzerland) · 2018Review
- Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics.Nucleic acids research · 2018Article
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Authors and funding
6 authors.
Funding
Abstract
motivationMany drugs interact with numerous proteins besides their intended therapeutic targets and a substantial portion of these interactions is yet to be elucidated. Protein-Drug Interaction Database (PDID) addresses incompleteness of these data by providing access to putative protein-drug interactions that cover the entire structural human proteome.
resultsPDID covers 9652 structures from 3746 proteins and houses 16 800 putative interactions generated from close to 1.1 million accurate, all-atom structure-based predictions for several dozens of popular drugs. The predictions were generated with three modern methods: ILbind, SMAP and eFindSite. They are accompanied by propensity scores that quantify likelihood of interactions and coordinates of the putative location of the binding drugs in the corresponding protein structures. PDID complements the current databases that focus on the curated interactions and the BioDrugScreen database that relies on docking to find putative interactions. Moreover, we also include experimentally curated interactions which are linked to their sources: DrugBank, BindingDB and Protein Data Bank. Our database can be used to facilitate studies related to polypharmacology of drugs including repurposing and explaining side effects of drugs. AVAILABILITY AND IMPLEMENTATION: PDID database is freely available at http://biomine.ece.ualberta.ca/PDID/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.