论文标题
分析元素和元素模拟的元动力模拟结果
Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d
论文作者
论文摘要
分子模拟求解了分子系统运动方程，通过添加时间坐标来使分子的3D形状四维形状。这些方法在药物发现中具有巨大的潜力，因为它们可以实际对药物靶向的蛋白质分子的结构以及潜在药物与其分子靶靶的结合过程进行建模。但是，这种方法的非常高的计算成本阻碍了生物分子模拟的常规应用。已经开发了几种解决这个问题的方法。其中之一，元动力学，消除已经访问过的模拟系统的状态，从而迫使该系统探索新州和新状态。在这里，我们介绍包装元数据剂和元元素3D，以分析和可视化元动力学的结果，尤其是由流行的元动力包装套装的元动力学的结果。
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically model the structures of protein molecules targeted by drugs as well as the process of binding of a potential drug to its molecular target. However, routine application of biomolecular simulations is hampered by the very high computational costs of this method. Several methods have been developed to address this problem. One of them, metadynamics, disfavors states of the simulated system that have been already visited and thus forces the system to explore new and new states. Here we present the package metadynminer and metadynminer3d to analyze and visualize results from metadynamics, in particular those produced by a popular metadynamics package Plumed.
