NEW APPROACH FOR DETERMINING LOW-FREQUENCY NORMAL-MODES IN MACROMOLECULES
NEW APPROACH FOR DETERMINING LOW-FREQUENCY NORMAL-MODES IN MACROMOLECULES
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DOI：
10.1002/bip.360340608
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发表时间：
1994-06-01
期刊：
影响因子：
2.9
通讯作者：
SANEJOUAND, YH
中科院分区：
文献类型：
--
作者：
DURAND, P;TRINQUIER, G;SANEJOUAND, YH
本文提出了一种计算大分子低频简正模的新方法，并将其应用于蛋白质。在第一步中，蛋白质链被划分成一个或多个残基的块，并且通过结合每个块的局部平移和旋转来在低分辨率水平下评估低频模式。在第二步中，这些低分辨率模式被在每个块中明确计算的高频模式扰动，从而导致精确的低频模式。该程序进行了测试的三种情况下，decaalanine，icosaleucin，和crambin使用扰动迭代计划在第二步。收敛性和数值精度进行评估和测试的各种分区。在第一步中获得的低分辨率模式总是被发现是很好的开始近似。该方法的潜在优点包括中央处理单元时间大约N-2取决于问题的大小（N是自由度的数量），使用并行处理的可能性，不需要将完整的质量加权二阶导数输入矩阵加载到中央存储器中，以及在该过程中引入进一步的结构层次结构，如二级结构或图案的可能性。此外，算法的任何改进或细化都得益于有效哈密顿理论的有效形式。(C)John Wiley & Sons，Inc.
A new method for calculating a set of low-frequency normal modes in macromolecules is proposed and applied to the case of proteins. In a first step, the protein chain is partitioned into blocks of one or more residues and the low-frequency modes are evaluated at a low-resolution level by combining the local translations and rotations of each block. In a second step, these low-resolution modes are perturbed by high-frequency modes explicitly calculated in each block, thus leading to the exact low-frequency modes. The procedure is tested for three cases-decaalanine, icosaleucin, and crambin-using a perturbation-iteration scheme in the second step. Convergence properties and numerical accuracy are assessed and tested for various partitions. The low-resolution modes obtained in the first step are always found to be good starting approximations. Potential advantages of the method include a central processing unit time roughly N-2 dependent on the size of the problem (N being the number of degrees of freedom), the possibility of using parallel processing, the nonrequirement for loading the complete mass-weighted second-derivative input matrix into central memory, and the possibility of introducing in the procedure further structural hierarchy, such as secondary structures or motifs. In addition, any improvement or refinement of the algorithm benefits from the efficient formalism of the effective Hamiltonian theory. (C) 1994 John Wiley & Sons, Inc.