A new hybrid Monte Carlo algorithm for protein potential function test and structure refinement
A new hybrid Monte Carlo algorithm for protein potential function test and structure refinement
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一种用于蛋白质势函数测试和结构细化的新型混合蒙特卡罗算法
DOI：
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发表时间：
1999
期刊：
影响因子：
--
通讯作者：
Hongyu Zhang
中科院分区：
文献类型：
--
作者：
Hongyu Zhang
一种新的混合蒙特卡罗（HMC）算法已经开发出来测试蛋白质的潜在功能，并最终完善蛋白质结构。该算法的主要原理是，在每个循环中，通过一组随机参数（包括分子动力学时间步长、分子动力学步数、分子动力学温度和初始分子动力学速度分配种子）进行短周期的分子动力学（MD）迭代，生成一个新的试验构象；然后根据Metropolis标准接受或拒绝新的构象。本文的新颖之处在于，MD迭代中的势与MC迭代中的势不同。前者是分子力学势，后者是基于知识的势。在KBP的指导下，利用MD迭代在构象空间中搜索具有低KBP能量的真实构象。它避免了在MD模拟中直接使用KBP函数的困难，因为KBP函数通常是不完整的，并且并不总是具有计算力所需的连续导数。新算法已在构象空间探测中得到验证。在这些测试计算中，发现KBP能量低于天然构象的值，并且均方根偏差（RMSD）与KBP能量之间的相关性显示与其他参考文献中的测试结果不同。目前，该算法可用于测试新的KBP函数。此外，如果能够找到一个天然构象能量最低且能量/RMSD相关性良好的KBP函数，那么该新算法也将成为改进基于理论的结构模型的工具。蛋白质1999;34:464 - 471。©1999 Wiley‐Liss, Inc。
A new Hybrid Monte Carlo (HMC) algorithm has been developed to test protein potential functions and, ultimately, refine protein structures. The main principle of this algorithm is, in each cycle, a new trial conformation is generated by carrying out a short period of molecular dynamics (MD) iterations with a set of random parameters (including the MD time step, the number of MD steps, the MD temperature, and the seed for initial MD velocity assignment); then to accept or reject the new conformation on the basis of the Metropolis criterion. The novelty in this paper is that the potential in MD iterations is different from that in the MC step. In the former, it is a molecular mechanics potential, in the latter it is a knowledge‐based potential (KBP). Directed by the KBP, the MD iteration is used to search conformational space for realistic conformations with low KBP energy. It circumvents the difficulty in using KBP functions directly in MD simulation, as KBP functions are typically incomplete, and do not always have continuous derivatives required for the calculation of the forces. The new algorithm has been tested in explorations of conformational space. In these test calculations the KBP energy was found to drop below the value for the native conformation, and the correlation between the root mean square deviation (RMSD) and the KBP energy was shown to be different from the test results in other references. At the present time, the algorithm is useful for testing new KBP functions. Furthermore, if a KBP function can be found for which the native conformation has the lowest energy and the energy/RMSD correlation is good, then this new algorithm also will be a tool for refinement of the theory‐based structural models. Proteins 1999;34:464–471. © 1999 Wiley‐Liss, Inc.
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DOI：
10.1093/protein/9.8.637
发表时间：
1996-08-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
DeBolt, SE;Skolnick, J
通讯作者：
Skolnick, J
影响因子：
5.6
作者：
Park, B;Levitt, M
通讯作者：
Levitt, M
影响因子：
5.6
作者：
Park, BH;Huang, ES;Levitt, M
通讯作者：
Levitt, M
影响因子：
5.6
作者：
Huang, ES;Subbiah, S;Levitt, M
通讯作者：
Levitt, M
影响因子：
56.9
作者：
BOCZKO, EM;BROOKS, CL
通讯作者：
BROOKS, CL