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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W480-4. doi: 10.1093/nar/gkp431. Epub 2009 May 22.

The SALAMI protein structure search server.

Author information

1
Centre for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146 Hamburg, Germany. margraf@zbh.uni-hamburg.de

Abstract

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.

PMID:
19465380
PMCID:
PMC2703935
DOI:
10.1093/nar/gkp431
[Indexed for MEDLINE]
Free PMC Article
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