基于球极坐标划分的蛋白质结构相似性比较

Similarity Comparison of Protein Structures via Protein Space Partition in Spherical Polar Coordinates

为了指导新药探索,减少耗费过高的实验次数,需要有一个准确、快速的分子相似性判定方法来选择待比较的分子.为此提出一种蛋白质结构相似性比较方法,使用空间球极坐标3个分量划分蛋白质所在区域,得到蛋白质基本组成元素的空间密度特征,进而判定2个蛋白质结构的相似性.实验结果表明,该方法可作为各种结构蛋白质相似性比较的辅助手段,不仅能较好地反映蛋白质分子的空间结构特征,而且还有令人满意的时间复杂性,对大分子的相似性比较及进一步分类将有重要意义.

In order to provide some guidance for the research of new drugs and to reduce the time of expensive experiments, a fast approach for the evaluation of structural similarity is needed to select the proteins to compare. A novel method for comparing protein structure similarity is proposed in this work. By partitioning the protein space in spherical polar coordinates, the space density of the main elements in protein molecules could be obtained easily and quickly. With the help of density fingerprints, the similarity between the proteins could be computed. The experimental results show that the proposed method could be used in similarity determination for proteins. Moreover, the principle of classification of the proteins of different functions based on their density fingerprints seems quite reasonable and applicable to other related applications, for example, it might be of significance in similarity determination and further classification for macromolecules.