Paper Info
Title
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome.
Abstract
Motivation: Many 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. Results: PDID 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.
Year
DOI
Venue
2016
10.1093/bioinformatics/btv597
BIOINFORMATICS
Field
DocType
Volume
Data mining,Human proteome project,Repurposing,Computer science,Docking (dog),Proteome,Bioinformatics,Protein Data Bank,BindingDB,Database,Protein structure,DrugBank
Journal
32
Issue
ISSN
Citations 
4
1367-4803
7
PageRank 
References 
Authors
0.47
34
6
Name
Order
Citations
PageRank
Chen Wang170.47
Gang Hu2112.56
Kui Wang3202.41
Michal Brylinski4376.10
Lei Xie544139.48
Lukasz A. Kurgan6102545.13