Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748, Garching, Germany.
J Comput Chem. 2014 Jan 15;35(2):150-8. doi: 10.1002/jcc.23476. Epub 2013 Oct 31.
A Hamiltonian Replica-Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two-dimensional backbone and one-dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions.
一种哈密顿 Replica-Exchange 分子动力学（REMD）模拟方法已经被开发出来，该方法使用二维主链和一维侧链偏置势，专门促进肽中的构象转变。为了最优地利用复制框架，在模拟过程中适当调整了每个副本中偏置势的水平。这导致相邻副本之间的交换率很高，并且提高了每个副本中所有构象的占有率/流动性。该方法的性能在几个肽和蛋白质系统上进行了测试，并与常规 MD 模拟和以前的 REMD 研究进行了比较。在无约束的蛋白质和肽折叠模拟以及限制环侧翼蛋白质区域的流动性的环结构精修中，观察到相关构象状态的采样得到了改善。
