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The SALAMI protein structure search server - PubMed

. 2009 Jul;37(Web Server issue):W480-4.

doi: 10.1093/nar/gkp431. Epub 2009 May 22.

Affiliations

PMID: 19465380
PMCID: PMC2703935
DOI: 10.1093/nar/gkp431

The SALAMI protein structure search server

Thomas Margraf et al. Nucleic Acids Res. 2009 Jul.

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.

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Figures

**Figure 1.**
Sensitivity of servers using 1WOT as a query. For each rank on x-axis, each point shows the number of true positives divided by the rank. Servers (DALI, VAST and SALAMI) are marked as shown in the key. Lines joining the points have no meaning and only serve to guide the eye.

**Figure 2.**
Sensitivity of servers using 1QLW as a query. Markers and servers as in Figure 1.

**Figure 3.**
Sensitivity of servers using 1WK2 as a query. Markers and servers as in Figure 1.

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