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The SALAMI protein structure search server

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 informatio...

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Detalles Bibliográficos
Autores principales: Margraf, Thomas, Schenk, Gundolf, Torda, Andrew E.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703935/
https://www.ncbi.nlm.nih.gov/pubmed/19465380
http://dx.doi.org/10.1093/nar/gkp431
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author Margraf, Thomas
Schenk, Gundolf
Torda, Andrew E.
author_facet Margraf, Thomas
Schenk, Gundolf
Torda, Andrew E.
author_sort Margraf, Thomas
collection PubMed
description 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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spelling pubmed-27039352009-07-01 The SALAMI protein structure search server Margraf, Thomas Schenk, Gundolf Torda, Andrew E. Nucleic Acids Res Articles 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. Oxford University Press 2009-07-01 2009-05-22 /pmc/articles/PMC2703935/ /pubmed/19465380 http://dx.doi.org/10.1093/nar/gkp431 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Articles
Margraf, Thomas
Schenk, Gundolf
Torda, Andrew E.
The SALAMI protein structure search server
title The SALAMI protein structure search server
title_full The SALAMI protein structure search server
title_fullStr The SALAMI protein structure search server
title_full_unstemmed The SALAMI protein structure search server
title_short The SALAMI protein structure search server
title_sort salami protein structure search server
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703935/
https://www.ncbi.nlm.nih.gov/pubmed/19465380
http://dx.doi.org/10.1093/nar/gkp431
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