Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities
Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities
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DOI：
10.1093/bioinformatics/btm073
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发表时间：
2007-05-01
期刊：
影响因子：
5.8
通讯作者：
Blundell, Tom L.
中科院分区：
文献类型：
--
作者：
Smith, Richard E.;Lovell, Simon C.;Blundell, Tom L.
动机：在计算蛋白质建模和设计中，侧链的精确定位涉及到大量旋转异构体组合的搜索，结果：我们将结构对齐的同源家族中包含的信息，以保守的卡角保守规则的形式，应用于比较建模的问题。这允许准确借用整个侧链构象和/或限制高概率旋转异构体箱。这些规则的应用一致地将需要搜索的旋转异构体组合的数量减少到微不足道的值，并且还减少了最终模型的总体侧链均方根偏差（rmsd）。该方法是补充目前的侧链布局算法，使用相互作用的集群的分解，以提高放置过程的速度。
Motivation: The accurate placement of side chains in computational protein modeling and design involves the searching of vast numbers of rotamer combinations.Results: We have applied the information contained within structurally aligned homologous families, in the form of conserved chi angle conservation rules, to the problem of the comparative modeling. This allows the accurate borrowing of entire side-chain conformations and/or the restriction to high probability rotamer bins. The application of these rules consistently reduces the number of rotamer combinations that need to be searched to trivial values and also reduces the overall side-chain root mean square deviation (rmsd) of the final model. The approach is complementary to current side-chain placement algorithms that use the decomposition of interacting clusters to increase the speed of the placement process.