ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority... Patterns observed by examining the evolutionary relationships among proteins of common origin can reveal the structural and functional importance of specific residue positions. In particular, amino acids that are highly conserved (i.e., their positions evolve at a slower rate than other positions) are particularly likely to be of biological importance, for example, for ligand binding. ConSurf is a bioinformatics tool for accurately estimating the evolutionary rate of each position in a protein family. Here we introduce a new release of ConSurf-DB, a database of precalculated ConSurf evolutionary conservation profiles for proteins of known structure. ConSurf-DB provides high-accuracy estimates of the evolutionary rates of the amino acids in each protein. A reliable estimate of a query protein's evolutionary rates depends on having a sufficiently large number of effective homologues (i.e., nonredundant yet sufficiently similar). With current sequence data, ConSurf-DB covers 82% of the PDB proteins. It will be updated on a regular basis to ensure that coverage remains high-and that it might even increase. Much effort was dedicated to improving the user experience. The repository is available at https://consurfdb.tau.ac.il/. BROADER AUDIENCE: By comparing a protein to other proteins of similar origin, it is possible to determine the extent to which each amino acid position in the protein evolved slowly or rapidly. A protein's evolutionary profile can provide valuable insights: For example, amino acid positions that are highly conserved (i.e., evolved slowly) are particularly likely to be of structural and/or functional importance, for example, for ligand binding and catalysis. We introduce here a new and improved version of ConSurf-DB, a continually updated database that provides precalculated evolutionary profiles of proteins with known structure. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Protein science : a publication of the Protein Society Pubmed

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

Protein science : a publication of the Protein Society: 1 – Nov 22, 2019
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ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

Protein science : a publication of the Protein Society: 1 – Nov 22, 2019

Abstract

Patterns observed by examining the evolutionary relationships among proteins of common origin can reveal the structural and functional importance of specific residue positions. In particular, amino acids that are highly conserved (i.e., their positions evolve at a slower rate than other positions) are particularly likely to be of biological importance, for example, for ligand binding. ConSurf is a bioinformatics tool for accurately estimating the evolutionary rate of each position in a protein family. Here we introduce a new release of ConSurf-DB, a database of precalculated ConSurf evolutionary conservation profiles for proteins of known structure. ConSurf-DB provides high-accuracy estimates of the evolutionary rates of the amino acids in each protein. A reliable estimate of a query protein's evolutionary rates depends on having a sufficiently large number of effective homologues (i.e., nonredundant yet sufficiently similar). With current sequence data, ConSurf-DB covers 82% of the PDB proteins. It will be updated on a regular basis to ensure that coverage remains high-and that it might even increase. Much effort was dedicated to improving the user experience. The repository is available at https://consurfdb.tau.ac.il/. BROADER AUDIENCE: By comparing a protein to other proteins of similar origin, it is possible to determine the extent to which each amino acid position in the protein evolved slowly or rapidly. A protein's evolutionary profile can provide valuable insights: For example, amino acid positions that are highly conserved (i.e., evolved slowly) are particularly likely to be of structural and/or functional importance, for example, for ligand binding and catalysis. We introduce here a new and improved version of ConSurf-DB, a continually updated database that provides precalculated evolutionary profiles of proteins with known structure.
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DOI
10.1002/pro.3779

Abstract

Patterns observed by examining the evolutionary relationships among proteins of common origin can reveal the structural and functional importance of specific residue positions. In particular, amino acids that are highly conserved (i.e., their positions evolve at a slower rate than other positions) are particularly likely to be of biological importance, for example, for ligand binding. ConSurf is a bioinformatics tool for accurately estimating the evolutionary rate of each position in a protein family. Here we introduce a new release of ConSurf-DB, a database of precalculated ConSurf evolutionary conservation profiles for proteins of known structure. ConSurf-DB provides high-accuracy estimates of the evolutionary rates of the amino acids in each protein. A reliable estimate of a query protein's evolutionary rates depends on having a sufficiently large number of effective homologues (i.e., nonredundant yet sufficiently similar). With current sequence data, ConSurf-DB covers 82% of the PDB proteins. It will be updated on a regular basis to ensure that coverage remains high-and that it might even increase. Much effort was dedicated to improving the user experience. The repository is available at https://consurfdb.tau.ac.il/. BROADER AUDIENCE: By comparing a protein to other proteins of similar origin, it is possible to determine the extent to which each amino acid position in the protein evolved slowly or rapidly. A protein's evolutionary profile can provide valuable insights: For example, amino acid positions that are highly conserved (i.e., evolved slowly) are particularly likely to be of structural and/or functional importance, for example, for ligand binding and catalysis. We introduce here a new and improved version of ConSurf-DB, a continually updated database that provides precalculated evolutionary profiles of proteins with known structure.

Journal

Protein science : a publication of the Protein SocietyPubmed

Published: Nov 22, 2019

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