An integrated system for studying residue coevolution in proteins
An integrated system for studying residue coevolution in proteins
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DOI：
10.1093/bioinformatics/btm584
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发表时间：
2008-01-15
期刊：
影响因子：
5.8
通讯作者：
Gerstein, Mark
中科院分区：
文献类型：
--
作者：
Yip, Kevin Y.;Patel, Prianka;Gerstein, Mark
残基协同进化是最近出现的一个重要概念，特别是在蛋白质结构的背景下。虽然已经提出了许多不同的量化功能，但对它们的相对优势和劣势知之甚少。此外，微妙的算法细节阻碍了实现和比较它们。我们通过开发一个集成的在线系统来解决这个问题，该系统可以使用一套全面的常用评分函数进行比较分析，包括统计耦合分析（SCA），子集变异的显式可能性（ELSC），互信息和基于相关性的方法。一组数据预处理选项，包括序列加权，残基分组和序列，位点和位点对的过滤，以提高协同进化信号检测的灵敏度和特异性。总共有100多个评分变化。该系统还提供了用于研究协同进化分数与晶体结构的残基间距离之间的关系的设施，如果提供的话，这可能有助于理解蛋白质结构。
Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not much is known about their relative strengths and weaknesses. Also, subtle algorithmic details have discouraged implementing and comparing them. We addressed this issue by developing an integrated online system that enables comparative analyses with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods. A set of data preprocessing options are provided for improving the sensitivity and specificity of coevolution signal detection, including sequence weighting, residue grouping and the filtering of sequences, sites and site pairs. A total of more than 100 scoring variations are available. The system also provides facilities for studying the relationship between coevolution scores and inter-residue distances from a crystal structure if provided, which may help in understanding protein structures.