Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field.
Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field.
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DOI：
10.1093/protein/gzn056
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发表时间：
2008-12
期刊：
影响因子：
--
通讯作者：
Osman R
中科院分区：
文献类型：
--
作者：
Cui M;Mezei M;Osman R
我们已经开发了一种改进的局部移动蒙特卡罗循环抽样方法的循环预测。该方法基于侧链扭转角的简单移动和环骨架的局部移动生成环构象。为了减少能量评估的计算成本，我们开发了一个基于网格的力场来表示蛋白质环境和溶剂化效应。模拟退火已被用来提高效率的本地移动MC环采样和识别低能量环构象。预测质量是在一组已知晶体结构的蛋白质环上进行评估的，这些蛋白质环以前曾被其他人用来测试不同的环预测方法。结果表明，该方法可以重现的实验结果与RMSD在1.8范围内的所有测试用例。本文提出的局部移动MC环预测方法可用于同源性模型、柔性蛋白质-配体和蛋白质-蛋白质对接研究中环区域的质量改进。
We have developed an improved local move Monte Carlo loop sampling approach for loop predictions. The method generates loop conformations based on simple moves for the torsion angles of side chains and local moves for backbone of loops. To reduce the computational costs for energy evaluations, we developed a grid-based force field to represent the protein environment and solvation effect. Simulated annealing has been used to enhance the efficiency of the local move MC loop sampling and identify low-energy loop conformations. The prediction quality is evaluated on a set of protein loops with known crystal structure that has been previously used by others to test different loop prediction methods. The results show that this approach can reproduce the experimental results with the RMSD within 1.8 Å for all the test cases. The local move MC loop prediction approach developed here could be useful for improvement of the quality the loop regions in homology models, flexible protein-ligand and protein-protein docking studies.
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