vmdICE: A Plug-In for Rapid Evaluation of Molecular Dynamics Simulations using VMD
vmdICE: A Plug-In for Rapid Evaluation of Molecular Dynamics Simulations using VMD
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DOI：
10.1002/jcc.21581
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发表时间：
2010-12-01
影响因子：
3
通讯作者：
Schreiner, Wolfgang
中科院分区：
文献类型：
--
作者：
Knapp, Bernhard;Lederer, Nadja;Schreiner, Wolfgang
分子动力学是研究生物分子间相互作用的一种强有力的硅胶方法。它求解了牛顿在特定时间段内原子的运动方程，并产生了一个轨迹文件，其中包含了模拟过程中原子的不同空间排列。每个原子的运动和能量都被记录下来。对于这些关于生物医学含义的模拟轨迹的评估，有几种方法可用。三个著名的参数是均方根偏差(RMSD)、均方根波动(RMSF)和溶剂可达表面积(SASA)。在这里，我们提出了一个新的插件软件“视觉分子动力学”(VMD)，允许交互的3D表示的RMSD，RMSF和SASA，直接在分子上。一方面，我们的插件对于没有经验的用户来说很容易操作，另一方面，它为该领域的专家提供了一个快速而灵活的系统空间动态的图形印象。(C)2010威利期刊公司J Comput Chem 31：2868-2873,2010
Molecular dynamics (MD) is a powerful in silica method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2868-2873, 2010