RaptorX server: A Resource for Template-Based Protein Structure Modeling
RaptorX server: A Resource for Template-Based Protein Structure Modeling
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DOI：
10.1007/978-1-4939-0366-5_2
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发表时间：
2014-01-01
期刊：
影响因子：
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通讯作者：
Xu, Jinbo
中科院分区：
文献类型：
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作者：
Kaellberg, Morten;Margaryan, Gohar;Xu, Jinbo
新发现的蛋白质的功能特性是现代生物学的一个关键挑战。为此，氨基酸链的三维原子排列的计算建模通常在确定蛋白质在生物过程中的作用方面至关重要。我们提出了一个基于网络的协议RaptorX服务器（raptorx.uchicago.edu），用于自动蛋白质二级结构预测、基于模板的三级结构建模和概率比对采样，给定一个目标序列，RaptorX服务器能够通过一种新的非线性上下文特异性比对势和概率一致性算法检测到甚至是远程相关的模板序列。使用这里提出的协议，因此可以获得高质量的结构模型，许多靶蛋白质序列时，只有远亲的蛋白质结构域的实验解决的结构。目前，RaptorX服务器可以在大约30分钟内完成200个氨基酸目标序列的二级和三级结构预测。
Assigning functional properties to a newly discovered protein is a key challenge in modern biology. To this end, computational modeling of the three-dimensional atomic arrangement of the amino acid chain is often crucial in determining the role of the protein in biological processes. We present a community-wide web-based protocol, RaptorX server (http://raptorx.uchicago.edu), for automated protein secondary structure prediction, template-based tertiary structure modeling, and probabilistic alignment sampling.Given a target sequence, RaptorX server is able to detect even remotely related template sequences by means of a novel nonlinear context-specific alignment potential and probabilistic consistency algorithm. Using the protocol presented here it is thus possible to obtain high-quality structural models for many target protein sequences when only distantly related protein domains have experimentally solved structures. At present, RaptorX server can perform secondary and tertiary structure prediction of a 200 amino acid target sequence in approximately 30 min.