The PDBbind Database: Methodologies and Updates

We have developed the PDBbind database to provide a comprehensive collection of binding affinities for the protein−ligand complexes in the Protein Data Bank (PDB). This paper gives a full description of the latest version, i.e., version 2003, which is an update to our recently reported work. Out of...

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Veröffentlicht in:	Journal of medicinal chemistry 2005-06, Vol.48 (12), p.4111-4119
Hauptverfasser:	Wang, Renxiao, Fang, Xueliang, Lu, Yipin, Yang, Chao-Yie, Wang, Shaomeng
Format:	Artikel
Sprache:	eng
Schlagworte:	Biological and medical sciences Databases, Protein Internet Ligands Medical sciences Miscellaneous Pharmacology. Drug treatments Protein Binding Proteins - chemistry
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container_end_page	4119
container_issue	12
container_start_page	4111
container_title	Journal of medicinal chemistry
container_volume	48
creator	Wang, Renxiao Fang, Xueliang Lu, Yipin Yang, Chao-Yie Wang, Shaomeng
description	We have developed the PDBbind database to provide a comprehensive collection of binding affinities for the protein−ligand complexes in the Protein Data Bank (PDB). This paper gives a full description of the latest version, i.e., version 2003, which is an update to our recently reported work. Out of 23 790 entries in the PDB release No.107 (January 2004), 5897 entries were identified as protein−ligand complexes that meet our definition. Experimentally determined binding affinities (K d, K i, and IC50) for 1622 of these were retrieved from the references associated with these complexes. A total of 900 complexes were selected to form a “refined set”, which is of particular value as a standard data set for docking and scoring studies. All of the final data, including binding affinity data, reference citations, and processed structural files, have been incorporated into the PDBbind database accessible on-line at http:// www.pdbbind.org/.
doi_str_mv	10.1021/jm048957q
format	Article
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Drug treatments</topic><topic>Protein Binding</topic><topic>Proteins - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Renxiao</creatorcontrib><creatorcontrib>Fang, Xueliang</creatorcontrib><creatorcontrib>Lu, Yipin</creatorcontrib><creatorcontrib>Yang, Chao-Yie</creatorcontrib><creatorcontrib>Wang, Shaomeng</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of medicinal chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Renxiao</au><au>Fang, Xueliang</au><au>Lu, Yipin</au><au>Yang, Chao-Yie</au><au>Wang, Shaomeng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The PDBbind Database: Methodologies and Updates</atitle><jtitle>Journal of medicinal chemistry</jtitle><addtitle>J. Med. Chem</addtitle><date>2005-06-16</date><risdate>2005</risdate><volume>48</volume><issue>12</issue><spage>4111</spage><epage>4119</epage><pages>4111-4119</pages><issn>0022-2623</issn><eissn>1520-4804</eissn><coden>JMCMAR</coden><abstract>We have developed the PDBbind database to provide a comprehensive collection of binding affinities for the protein−ligand complexes in the Protein Data Bank (PDB). This paper gives a full description of the latest version, i.e., version 2003, which is an update to our recently reported work. Out of 23 790 entries in the PDB release No.107 (January 2004), 5897 entries were identified as protein−ligand complexes that meet our definition. Experimentally determined binding affinities (K d, K i, and IC50) for 1622 of these were retrieved from the references associated with these complexes. A total of 900 complexes were selected to form a “refined set”, which is of particular value as a standard data set for docking and scoring studies. 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subjects	Biological and medical sciences Databases, Protein Internet Ligands Medical sciences Miscellaneous Pharmacology. Drug treatments Protein Binding Proteins - chemistry
title	The PDBbind Database: Methodologies and Updates
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