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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

Database Description

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


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)

Subcategory: Small molecules

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