Nucleic Acids Research, 2005, Vol. 33, Database issue D238-D241
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
Research and Development, IDR Tech. B-3003 Tripolis, 210 KumGok-Dong, BunDang-Ku, SungNam-Shi, KyungKi-Do, Republic of Korea 463-805
* To whom correspondence should be addressed. Tel: +82 31 728 0500; Fax: +82 31 728 0503; Email: jms{at}idrtech.com
Received June 30, 2004; Revised and Accepted October 4, 2004
PDB-Ligand (http://www.idrtech.com/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). It is also a database tool that allows one to browse, classify, superimpose and visualize these structures. As of May 2004, there are about 4870 types of small molecular ligands, experimentally determined as a complex with protein or DNA in the PDB. The proteins that a given ligand binds are often homologous and present the same binding structure to the ligand. However, there are also many instances wherein a given ligand binds to two or more unrelated proteins, or to the same or homologous protein in different binding environments. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in the PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on a simple and flexible ligand clustering method. PDB-Ligand will be a good resource for both a better interpretation of ligand-binding structures and the development of better scoring functions to be used in many drug discovery applications.
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