Improved prediction of protein side-chain conformations with SCWRL4.
Improved prediction of protein side-chain conformations with SCWRL4.
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DOI：
10.1002/prot.22488
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发表时间：
2009-12
影响因子：
2.9
通讯作者：
Dunbrack, Roland L., Jr.
中科院分区：
文献类型：
--
作者：
Krivov, Georgii G.;Shapovalov, Maxim V.;Dunbrack, Roland L., Jr.
侧链构象的确定是蛋白质结构预测和蛋白质设计的重要一步，尽管只有少量的宽度是一种这样的方法。由于它的速度，准确性和易用性而流行，因此，可以通过以下速度来实现更高的准确性。 1）基于内核密度估计的新型旋转库；原子 - 原子相互作用的潜力；使用晶体链的晶体密度的晶体算子的相互作用图表明，具有较高电子密度的侧链比具有低电子密度和构象障碍的侧链更容易预测在X射线位置的40°内，正确预测了379种蛋白质，χ1角的86％和75％的测试集随着电子密度较高（25-100个百分点），这些数字上升到89％和80％。其他软件程序。
Determination of side-chain conformations is an important step in protein structure prediction and protein design. Many such methods have been presented, although only a small number are in widespread use. SCWRL is one such method, and the SCWRL3 program (2003) has remained popular due to its speed, accuracy, and ease-of-use for the purpose of homology modeling. However, higher accuracy at comparable speed is desirable. This has been achieved through: 1) a new backbone-dependent rotamer library based on kernel density estimates; 2) averaging over samples of conformations about the positions in the rotamer library; 3) a fast anisotropic hydrogen bonding function; 4) a short-range, soft van der Waals atom-atom interaction potential; 5) fast collision detection using k-discrete oriented polytopes; 6) a tree decomposition algorithm to solve the combinatorial problem; and 7) optimization of all parameters by determining the interaction graph within the crystal environment using symmetry operators of the crystallographic space group. Accuracies as a function of electron density of the side chains demonstrate that side chains with higher electron density are easier to predict than those with low electron density and presumed conformational disorder. For a testing set of 379 proteins, 86% of χ1 angles and 75% of χ1+2 are predicted correctly within 40° of the X-ray positions. Among side chains with higher electron density (25th–100th percentile), these numbers rise to 89% and 80%. The new program maintains its simple command-line interface, designed for homology modeling, and is now available as a dynamic-linked library for incorporation into other software programs.
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影响因子：
5.8
作者：
Kingsford, CL;Chazelle, B;Singh, M
通讯作者：
Singh, M
DOI：
10.1073/pnas.87.12.4468
发表时间：
1990-06-01
影响因子：
11.1
作者：
KOSSIAKOFF, AA;SHPUNGIN, J;SINTCHAK, MD
通讯作者：
SINTCHAK, MD
影响因子：
8
作者：
Dahiyat, BI;Mayo, SL
通讯作者：
Mayo, SL
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
5.6
作者：
Gray, JJ;Moughon, S;Baker, D
通讯作者：
Baker, D