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Nucleic Acids Research Advance Access originally published online on December 1, 2006
Nucleic Acids Research 2007 35(Database issue):D198-D201; doi:10.1093/nar/gkl999
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Nucleic Acids Research, 2007, Vol. 35, Database issue D198-D201
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities

Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen and Michael K. Gilson*

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute 9600 Gudelsky Drive, Rockville, MD 20850, USA

*To whom correspondence should be addressed. Tel: +1 240 314 6217; Fax: +1 240 314 6255; Email: gilson{at}umbi.umd.edu

Received August 11, 2006. Revised October 18, 2006. Accepted October 20, 2006.

BindingDB (http://www.bindingdb.org) is a publicly accessible database currently containing ~20 000 experimentally determined binding affinities of protein–ligand complexes, for 110 protein targets including isoforms and mutational variants, and ~11 000 small molecule ligands. The data are extracted from the scientific literature, data collection focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in the Protein Data Bank. The BindingDB website supports a range of query types, including searches by chemical structure, substructure and similarity; protein sequence; ligand and protein names; affinity ranges and molecular weight. Data sets generated by BindingDB queries can be downloaded in the form of annotated SDfiles for further analysis, or used as the basis for virtual screening of a compound database uploaded by the user. The data in BindingDB are linked both to structural data in the PDB via PDB IDs and chemical and sequence searches, and to the literature in PubMed via PubMed IDs.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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