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Nucleic Acids Research 2005 33(Web Server Issue):W303-W305; doi:10.1093/nar/gki409
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© The Author 2005. 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}oupjournals.org

Article

SRide: a server for identifying stabilizing residues in proteins

Csaba Magyar, M. Michael Gromiha1, Gerard Pujadas2, Gábor E. Tusnády1 and István Simon*

Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences H-1518 Budapest, PO Box 7, Hungary 1Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan 2Research group in ‘Wine and Health’, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili Campus de Sant Pere Sescelades s/n, Tarragona 43007, Catalonia, Spain

*To whom correspondence should be addressed. Tel: +36 1 4669276; Fax: +36 1 4665465, Email: simon{at}enzim.hu

Received February 11, 2005. Revised March 21, 2005. Accepted March 21, 2005.

Residues expected to play key roles in the stabilization of proteins [stabilizing residues (SRs)] are selected by combining several methods based mainly on the interactions of a given residue with its spatial, rather than its sequential neighborhood and by considering the evolutionary conservation of the residues. A residue is selected as a stabilizing residue if it has high surrounding hydrophobicity, high long-range order, high conservation score and if it belongs to a stabilization center. The definition of all these parameters and the thresholds used to identify the SRs are discussed in detail. The algorithm for identifying SRs was originally developed for TIM-barrel proteins [M. M. Gromiha, G. Pujadas, C. Magyar, S. Selvaraj, and I. Simon (2004), Proteins, 55, 316–329] and is now generalized for all proteins of known 3D structure. SRs could be applied in protein engineering and homology modeling and could also help to explain certain folds with significant stability. The SRide server is located at http://sride.enzim.hu.


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