PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures.
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.
Shin
Jae-Min
JM
Research and Development, IDR Tech. B-3003 Tripolis, 210 KumGok-Dong, BunDang-Ku, SungNam-Shi, KyungKi-Do, Republic of Korea 463-805. jms@idrtech.com
Cho
Doo-Ho
DH
D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D030562:Databases, Protein; D008024:Ligands; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
D008024:Ligands; D011506:Proteins; D000255:Adenosine Triphosphate