The Phyre2 web portal for protein modeling, prediction and analysis.
The Phyre2 web portal for protein modeling, prediction and analysis.
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DOI：
10.1038/nprot.2015.053
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发表时间：
2015-06
期刊：
影响因子：
14.8
通讯作者：
Sternberg MJ
中科院分区：
文献类型：
--
作者：
Kelley LA;Mezulis S;Yates CM;Wass MN;Sternberg MJ
Phyre2是一套网络工具，用于预测和分析蛋白质结构，功能和突变。Phyre2的重点是为生物学家提供一个简单直观的界面，以使用最先进的蛋白质生物信息学工具。Phyre2取代了Phyre，这是我们之前发布的协议的原始版本。在这个更新的协议中，我们描述了Phyre2，它使用先进的远程同源性检测方法来构建3D模型，预测配体结合位点，并分析氨基酸变体（例如nsSNP）对用户蛋白质序列的影响。用户通过一个简单的界面在他们确定的详细程度上引导结果。该协议将指导用户从提交蛋白质序列到解释其模型的二级和三级结构，其结构域组成和模型质量。描述了一系列额外的可用工具，以找到基因组中的蛋白质结构，一次提交大量序列，并每周自动搜索难以建模的蛋白质。该服务器位于http://www.sbg.bio.ic.ac.uk/phyre2。一个典型的结构预测将在提交后30分钟至2小时内返回。
Phyre2 is a suite of tools available on the web to predict and analyse protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a protocol. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyse the effect of amino-acid variants (e.g. nsSNPs) for a user’s protein sequence. Users are guided through results by a simple interface at a level of detail determined by them. This protocol will guide a user from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30mins and 2 hours after submission.