一种自动确定蛋白质结构中疏水核心的方法。
A procedure for the automatic determination of hydrophobic cores in protein structures.
作者信息
Swindells M B
机构信息
Protein Engineering Research Institute, Osaka, Japan.
出版信息
Protein Sci. 1995 Jan;4(1):93-102. doi: 10.1002/pro.5560040112.
Abstract
An algorithm is described for automatically detecting hydrophobic cores in proteins of known structure. Three pieces of information are considered in order to achieve this goal. These are: secondary structure, side-chain accessibility, and side-chain-side-chain contacts. Residues are considered to contribute to a core when they occur in regular secondary structure and have buried side chains that form predominantly nonpolar contacts with one another. This paper describes the algorithm's application to families of proteins with conserved topologies but low sequence similarities. The aim of this investigation is to determine the efficacy of the algorithm as well as to study the extent to which similar cores are identified within a common topology.
摘要
本文描述了一种用于自动检测已知结构蛋白质中疏水核心的算法。为实现这一目标，考虑了三条信息。它们是：二级结构、侧链可及性和侧链-侧链接触。当残基出现在规则的二级结构中且具有埋藏的侧链，这些侧链彼此之间主要形成非极性接触时，就认为这些残基对核心有贡献。本文描述了该算法在具有保守拓扑结构但序列相似性较低的蛋白质家族中的应用。这项研究的目的是确定该算法的有效性，以及研究在共同拓扑结构中识别相似核心的程度。
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