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Protocols

PDTD specifications

Information


Unique identifier OMICS_05436
Name PDTD
Alternative name Potential Drug Target Database
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Registration required Yes
Maintained No

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Publications for Potential Drug Target Database

PDTD citations

 (18)
call_split

TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds

2018
Front Plant Sci
PMCID: 5827417
PMID: 29520288
DOI: 10.3389/fpls.2018.00211
call_split See protocol

[…] query in its background database, which is a large-scale pharmacophore repertoire curated from target information in TargetBank (in-house data in PharmMapper project), DrugBank (), BindingDB (), and PDTD (). The server PharmMapper can help to find the optimal mapping poses of the user-uploaded small molecules against all the target genes in PharmTargetDB and the top N potential candidates togethe […]

library_books

Docking based inverse virtual screening: methods, applications, and challenges

2018
Biophysics Rep
PMCID: 5860130
PMID: 29577065
DOI: 10.1007/s41048-017-0045-8

[…] l trial, and 1469 research targets. However, the TTD database does not provide 3D structures of the targets, which need to be downloaded from the PDB database by users.Potential drug–target database (PDTD) (Gao et al. ) is another database focusing on therapeutic targets. Different to TTD, PDTD contains only protein targets. Impressively, cleaned 3D structures for both protein and active sites are […]

library_books

Notoginsenoside R7 suppresses cervical cancer via PI3K/PTEN/Akt/mTOR signaling

2017
Oncotarget
PMCID: 5752536
PMID: 29312623
DOI: 10.18632/oncotarget.22721

[…] at using ChemOffice 2006 (Chem 3D). Individual PDB files were modified in AutoDock with MGLTools 1.5.6 (Scripps Institute). Crystal structures of the object-protein complexes derived from the TTD and PDTD were obtained from the PDB database. All non-standard molecules (including water molecules, ligands, and other heteroatoms) were removed from the protein structures using Chimera (version 1.10.2) […]

library_books

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database

2017
Nucleic Acids Res
PMCID: 5793840
PMID: 28472422
DOI: 10.1093/nar/gkx374

[…] ing fishing. PharmMapper is backed up by a large, internal collection of pharmacophore database, namely PharmTargetDB annotated from all the targets information in BindingDB, TargetBank, DrugBank and PDTD. Over 7000 receptor-based pharmacophore models (covering 1627 drug target information, 459 of which are human protein targets) are stored and accessed by PharmMapper. However, the number of struc […]

library_books

Discovery of the molecular mechanisms of the novel chalcone based Magnaporthe oryzae inhibitor C1 using transcriptomic profiling and co expression network analysis

2016
Springerplus
PMCID: 5075332
PMID: 27818889
DOI: 10.1186/s40064-016-3385-9

[…] A total of 73 common potential targets for compound C1 were identified using the three web server-based approaches (Fig. a). Following assessment for drug-ability using the Potential Drug Target Database (PDTD) (Liu et al. ), 185 proteins were predicted to be potential therapeutic targets by Tarfisdock. There were 190 and 206 potential targets predicted by DARA-CPI and P […]

library_books

Systems pharmacology to investigate the interaction of berberine and other drugs in treating polycystic ovary syndrome

2016
Sci Rep
PMCID: 4910093
PMID: 27306862
DOI: 10.1038/srep28089

[…] ng approach. The model is supported by a large repertoire of pharmacophore database composed of more than 7,000 receptor-based pharmacophore models extracted from Target-Bank, DrugBank, BindingDB and PDTD. It predicts the best mapping poses for a given query molecule against all the pharmacophore models using ligand-protein reverse docking approach. The result lists the topN best-fitted hits with […]

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PDTD institution(s)
Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, China; School of Pharmacy, East China University of Science and Technology, Shanghai, China
PDTD funding source(s)
Supported by the Special Fund for Major State Basic Research Project (grant 2002CB512802), the National Natural Science Foundation of China (grants 20721003 and 10572033), the 863 Hi-Tech Program of China (grant 2007AA02Z304) and the Shanghai Postdoctoral Scientific Program.

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