蛋白质原子运动轨迹生成改进算法

Algorithm Improvement of Generating Atomic'S Trajectory in Protein

传统实现蛋白质分子动态模拟均采用采样方式生成原子运动轨迹。较大的采样间距使原本光滑的轨迹由于时域影响变得凹凸,而小的采样间距使运动缓慢且难以辨别。为解决上述问题,提出一种基于主元分析的运动轨迹生成算法。在参考坐标系内采集所有原子位置数据,计算并构造位置差的协方差矩阵,选择主元构成新基作为投影向量,确定兴趣运动点。以PYP为例,实验验证,通过提出的算法仿真PYP运动平滑而又凸显重点。

The traditional protein dynamic simulation adopts the sampling method to generate atomic trajectory generally.Larger sample spacing may cause the smooth trajectory to convex affected by the time domain,then small sample spacing may cause the movement slowly and difficult to discern.To solve the problems,an algorithm based on principal component analysis to generate the trajectory was proposed.Position data of all atoms within the reference coordinate system were collected,the covariance matrix of all atoms＇s position distance was constructed,and the principal components were selected to construct the new vector as projection vector and determine the interesting points.As an example of Photosensitive Yellow Protein,the atomic movement in the protein show clearly.The PYP＇s movement is smooth and highlights the focus.