Computational basis of knowledge‐based conformational probabilities derived from local‐ and long‐range interactions in proteins
Computational basis of knowledge‐based conformational probabilities derived from local‐ and long‐range interactions in proteins
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来自蛋白质局部和远程相互作用的基于知识的构象概率的计算基础
DOI：
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发表时间：
2006
期刊：
影响因子：
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通讯作者：
B. Erman
中科院分区：
文献类型：
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作者：
L. Ormeci;A. Gursoy;Guzin Tunca;B. Erman
Ramachandran地图中各种盆地的概率被严格地检查。从分子计算和蛋白质文库两方面讨论了概率计算的理论基础。Ramachandran图中明确定义的盆地被视为旋转异构状态。讨论了肽链上不同残基状态的统计独立性和依赖性。Flory孤立对假说，近邻相关性，上下文效应和长期相关性进行了严格的检查。与早期的聚合物理论类似，介绍了一种评估螺旋和扩展序列中长距离相关性的方法。构建了三种不同的蛋白质文库，其中考虑了(i)卷曲区域的残基，（ii）所有区域的残基，以及（iii）仅考虑蛋白质的螺旋和延伸区域的残基。从这些库中计算的单线态和成对相关概率用于预测给定序列是螺旋还是扩展。使用成对依赖的预测并不比使用单线态概率的预测好。长期相关性的建模显著改善了预测结果。从数据集中去除变色龙序列也改善了预测，但程度较低。2007的蛋白质。©2006 Wiley‐Liss, Inc。
The probabilities of the various basins in Ramachandran maps are examined critically. The theoretical basis of probability calculations both from molecular computations and from protein libraries are discussed. The well‐defined basins of the Ramachandran maps are treated as rotational isomeric states. Statistical independence and dependence of the states of different residues along the peptide chain are discussed. The Flory isolated pair hypothesis, near neighbor correlations, context effects, and long‐range correlations are examined critically. A method of evaluating long‐range correlations in helical and extended sequences is introduced in analogy with earlier polymer theory. Three different protein libraries are constructed where data is considered from residues in the (i) coiled regions, (ii) all regions, and (iii) only the helical and extended regions of proteins. Singlet and pairwise dependent probabilities calculated from these libraries are used to predict whether a given sequence is helical or extended. Predictions using pairwise dependence were not better than those using singlet probabilities. Modeling of long‐range correlations improved the predictions significantly. Removal of the Chameleon sequences from the data set also improved the predictions, but to a lesser extent. Proteins 2007. © 2006 Wiley‐Liss, Inc.
影响因子：
2.9
作者：
Jha, AK;Colubri, A;Freed, KF
通讯作者：
Freed, KF
影响因子：
5.6
作者：
Zaman, MH;Shen, MY;Sosnick, TR
通讯作者：
Sosnick, TR