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Nucleic Acids Research 2006 34(Database Issue):D522-D526; doi:10.1093/nar/gkj039
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Nucleic Acids Research, 2006, Vol. 34, Database issue D522-D526
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

AffinDB: a freely accessible database of affinities for protein–ligand complexes from the PDB

Peter Block, Christoph A. Sotriffer, Ingo Dramburg and Gerhard Klebe*

Department of Pharmaceutical Chemistry, Philipps-University Marburg Marbacher Weg 6, D-35032 Marburg, Germany

*To whom correspondence should be addressed. Tel: +49 6421 2821313; Fax: +49 6421 2828994; Email: klebe{at}staff.uni-marburg.de

Received June 17, 2005. Revised October 3, 2005. Accepted October 3, 2005.

AffinDB is a database of affinity data for structurally resolved protein–ligand complexes from the Protein Data Bank (PDB). It is freely accessible at http://www.agklebe.de/affinity. Affinity data are collected from the scientific literature, both from primary sources describing the original experimental work of affinity determination and from secondary references which report affinity values determined by others. AffinDB currently contains over 730 affinity entries covering more than 450 different protein–ligand complexes. Besides the affinity value, PDB summary information and additional data are provided, including the experimental conditions of the affinity measurement (if available in the corresponding reference); 2D drawing, SMILES code and molecular weight of the ligand; links to other databases, and bibliographic information. AffinDB can be queried by PDB code or by any combination of affinity range, temperature and pH value of the measurement, ligand molecular weight, and publication data (author, journal and year). Search results can be saved as tabular reports in text files. The database is supposed to be a valuable resource for researchers interested in biomolecular recognition and the development of tools for correlating structural data with affinities, as needed, for example, in structure-based drug design.

Present address: Ingo Dramburg, BioSolveIT, An der Ziegelei 75, 53757 Sankt Augustin, Germany


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