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PDTD: a web-accessible protein database for drug target identification.
Zhenting Gao1, Honglin Li, Hailei Zhang
1Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. zhentg@mail.shcnc.ac.cn
BMC Bioinformatics
|February 20, 2008
Summary
A new Potential Drug Target Database (PDTD) aids drug discovery by integrating with TarFisDock for in silico target identification. This resource helps identify potential binding proteins for small molecules, accelerating drug development.
Area of Science:
- Computational chemistry and bioinformatics
- Drug discovery and development
Background:
- Target identification is crucial for modern drug discovery.
- Molecular docking and 3D protein structures are key tools for identifying potential drug targets.
- Existing tools require a reverse docking program and a drug target database.
Purpose of the Study:
- To develop and present the Potential Drug Target Database (PDTD) for in silico target identification.
- To integrate PDTD with the TarFisDock web server for enhanced drug target discovery.
- To provide a valuable resource for identifying binding proteins for small molecules.
Main Methods:
- Constructed PDTD, a web-accessible protein database with over 1100 entries and 3D structures from the Protein Data Bank.
- Extracted data from literature and databases (TTD, DrugBank, Thomson Pharma) for over 830 known or potential drug targets.
- Integrated PDTD with TarFisDock, enabling identification of binding proteins for small molecules using docking scores and downloadable results.
Main Results:
- PDTD contains comprehensive information on drug targets, including protein/active site structures (PDB, mol2), diseases, functions, and pathways.
- The database supports keyword searches (PDB ID, target name, disease name) and allows free download of data.
- The integration with TarFisDock allows for the identification of potential binding targets ranked by scoring.
Conclusions:
- PDTD is a unique and comprehensive repository for drug targets.
- The PDTD-TarFisDock integration facilitates in silico drug target identification and virtual screening.
- This platform supports the discovery of new drug uses and understanding pharmacological relevance.
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