NAR Molecular Biology Database Collection entry number 615
Jae-Min Shin and Doo-Ho Cho
Research and Development, IDR Tech. B-3003 Tripolis, 210 KumGok-Dong, BunDang-Ku, SungNam-Shi, KyungKi-Do, Republic of Korea 463-805
PDB-Ligand is a three dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). One unique feature of PDB-Ligand is that one can browse, classify, superimpose, and visualize the interactions between ligands and proteins. Currently, there are about 5,000 types of small molecular ligands, experimentally determined as a complex with protein or DNA in PDB. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on simple and flexible ligand clustering method. PDB-Ligand will be a good resource both for the better interpretation of ligand-binding structures and for the development of better scoring functions to be used in many drug discovery applications. PDB-Ligand is freely accessible through the URL at http://www.idrtech.com/PDB-Ligand/.
We thank SM Kim, CK Han, JH Yoon, YH In, and ND Kim for useful discussions and comments. We also thank YW Kim for website maintaining. This study was supported by a grant of Korean Health 21 R&D Project, Ministry of Health & Welfare, Republic of Korea. (Grant ID: 03-PJ2-PG4-BD02-0001)
Category: Structure Databases
Subcategory: Small molecules
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