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

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．