A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.
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DOI：
10.1016/j.str.2011.03.019
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发表时间：
2011-06-08
期刊：
影响因子：
5.7
通讯作者：
Dunbrack, Roland L., Jr.
中科院分区：
文献类型：
--
作者：
Shapovalov, Maxim V.;Dunbrack, Roland L., Jr.
旋转异构体库用于蛋白质结构测定、结构预测和设计。主链依赖性旋转异构体库由旋转异构体频率和它们的平均二面角以及作为主链二面角α和β的函数的方差组成。这个旋转异构体库的先前版本并没有考虑到平滑性，尽管一些结构预测和蛋白质设计方法将从平滑中受益。一个新版本的骨架依赖的旋转异构体库已经开发使用自适应内核密度估计的旋转异构体的频率和自适应内核回归的平均二面角和方差。提出的公式允许评估任何、ψ点处的旋转异构体概率、平均角度和方差，即作为和ψ的连续函数。连续的概率密度估计的非旋转异构的酰胺，羧酸酯，和芳香族侧链的自由度已被建模为骨干二面角和旋转异构体的其余自由度的函数。具有不同平滑水平的新的主链依赖性旋转异构体库可从http://dunbrack.fccc.edu获得。
Rotamer libraries are used in protein structure determination, structure prediction, and design. The backbone-dependent rotamer library consists of rotamer frequencies and their mean dihedral angles and variances as a function of the backbone dihedral angles ϕ and ψ. Previous versions of this rotamer library were not developed with smoothness in mind, although some structure prediction and protein design methods would strongly benefit from smoothing. A new version of the backbone-dependent rotamer library has been developed using adaptive kernel density estimates for the rotamer frequencies and adaptive kernel regression for the mean dihedral angles and variances. The formulation presented allows for evaluation of the rotamer probabilities, mean angles and variances at any ϕ, ψ point, i.e. as a continuous function of ϕ and ψ. Continuous probability density estimates for the non-rotameric degrees of freedom of amides, carboxylates, and aromatic side chains have been modeled as a function of the backbone dihedral angles and rotamers of the remaining degrees of freedom. New backbone-dependent rotamer libraries at varying levels of smoothing are available from http://dunbrack.fccc.edu.
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影响因子：
2.9
作者：
Krivov, Georgii G.;Shapovalov, Maxim V.;Dunbrack, Roland L., Jr.
通讯作者：
Dunbrack, Roland L., Jr.
影响因子：
56.9
作者：
Dahiyat, BI;Mayo, SL
通讯作者：
Mayo, SL
影响因子：
5.6
作者：
Calhoun, JR;Kono, H;Saven, JG
通讯作者：
Saven, JG
DOI：
10.1073/pnas.97.19.10383
发表时间：
2000-09-12
影响因子：
11.1
作者：
Kuhlman, B;Baker, D
通讯作者：
Baker, D
DOI：
10.1007/s10969-008-9045-8
发表时间：
2009-03
期刊：
Journal of structural and functional genomics
影响因子：
--
作者：
Headd, Jeffrey J;Immormino, Robert M;Keedy, Daniel A;Emsley, Paul;Richardson, David C;Richardson, Jane S
通讯作者：
Richardson, Jane S