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Nucleic Acids Research Advance Access published online on May 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp431
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© 2009 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.

Web Server Issue

The SALAMI protein structure search server

Thomas Margraf*, Gundolf Schenk and Andrew E. Torda

Centre for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146 Hamburg, Germany

*To whom correspondence should be addressed. Tel: +49 40 42838 7341; Fax: +49 40 42838 7332; Email: margraf{at}zbh.uni-hamburg.de

Received January 31, 2009. Revised April 30, 2009. Accepted May 11, 2009.

Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page lists the related proteins, details of the sequence and structure similarity and implied sequence alignments. Via a simple structure viewer, one can view superpositions of query and library structures and finally download superimposed coordinates. The alignment method is very tolerant of large gaps and insertions, and tends to produce slightly longer alignments than other similar programs.


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