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ConSurf-DB:一个可访问的数据库,用于存储 PDB 蛋白中大多数蛋白的进化保守模式。

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

机构信息

Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

出版信息

Protein Sci. 2020 Jan;29(1):258-267. doi: 10.1002/pro.3779. Epub 2019 Nov 22.

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.

摘要

通过检查具有共同起源的蛋白质之间的进化关系,可以揭示特定残基位置的结构和功能重要性。特别是高度保守的氨基酸(即,它们的位置比其他位置进化得更慢)很可能具有生物学重要性,例如配体结合。ConSurf 是一种用于准确估计蛋白质家族中每个位置进化速度的生物信息学工具。在这里,我们介绍了 ConSurf-DB 的新版本,这是一个预先计算的已知结构蛋白质的 ConSurf 进化保守性图谱数据库。ConSurf-DB 为每个蛋白质中的氨基酸提供了高精度的进化率估计。查询蛋白质的进化率的可靠估计取决于具有足够数量的有效同源物(即,非冗余但足够相似)。有了当前的序列数据,ConSurf-DB 涵盖了 82%的 PDB 蛋白质。它将定期更新,以确保覆盖率保持高水平,甚至可能增加。我们投入了大量精力来改善用户体验。该存储库可在 https://consurfdb.tau.ac.il/ 上获得。更广泛的受众:通过将蛋白质与其他具有相似起源的蛋白质进行比较,可以确定蛋白质中每个氨基酸位置进化缓慢或快速的程度。蛋白质的进化图谱可以提供有价值的见解:例如,高度保守的氨基酸位置(即进化缓慢)很可能具有结构和/或功能重要性,例如配体结合和催化。在这里,我们介绍了 ConSurf-DB 的一个新版本,这是一个不断更新的数据库,提供了具有已知结构的蛋白质的预先计算的进化图谱。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49d/6933843/8adfaa317d65/PRO-29-258-g001.jpg

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