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ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its...

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Autores principales: Landau, Meytal, Mayrose, Itay, Rosenberg, Yossi, Glaser, Fabian, Martz, Eric, Pupko, Tal, Ben-Tal, Nir
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160131/
https://www.ncbi.nlm.nih.gov/pubmed/15980475
http://dx.doi.org/10.1093/nar/gki370
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author Landau, Meytal
Mayrose, Itay
Rosenberg, Yossi
Glaser, Fabian
Martz, Eric
Pupko, Tal
Ben-Tal, Nir
author_facet Landau, Meytal
Mayrose, Itay
Rosenberg, Yossi
Glaser, Fabian
Martz, Eric
Pupko, Tal
Ben-Tal, Nir
author_sort Landau, Meytal
collection PubMed
description Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. ConSurf () is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. Structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. We present here version 3.0 of ConSurf. This new version includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. Various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. Moreover, ConSurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores.
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spelling pubmed-11601312005-06-29 ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures Landau, Meytal Mayrose, Itay Rosenberg, Yossi Glaser, Fabian Martz, Eric Pupko, Tal Ben-Tal, Nir Nucleic Acids Res Article Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. ConSurf () is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. Structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. We present here version 3.0 of ConSurf. This new version includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. Various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. Moreover, ConSurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores. Oxford University Press 2005-07-01 2005-06-27 /pmc/articles/PMC1160131/ /pubmed/15980475 http://dx.doi.org/10.1093/nar/gki370 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Landau, Meytal
Mayrose, Itay
Rosenberg, Yossi
Glaser, Fabian
Martz, Eric
Pupko, Tal
Ben-Tal, Nir
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
title ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
title_full ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
title_fullStr ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
title_full_unstemmed ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
title_short ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
title_sort consurf 2005: the projection of evolutionary conservation scores of residues on protein structures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160131/
https://www.ncbi.nlm.nih.gov/pubmed/15980475
http://dx.doi.org/10.1093/nar/gki370
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