An algorithm to measuring protein curvature based on the protein SES atoms

• 作 者: Yujiao Yan Xiaofeng Song
• 机 构: DepartmentofBiomedicalEngineering,NanjingUniversityofAeronauticsandAstronautics,Nanjing210016China
• 出 处: 第五届全国生物信息学与系统生物学学术大会
• 发表日期: 2012年8期
• 关键词: protein molecular surface curvature shape index protein-protein interaction dock

　　Molecular surface plays an important role in analyzing protein molecular structure and function.Analysis of protein-protein interaction sites using surface curvature and shape index is an important method to study the protein function based on molecular structure.Therefore, accurate calculations of molecular curvature are indispensable.This paper presents an algorithm to measuring protein surface curvature based on the protein molecular surface atoms.It calculates the normal vectors of surface atoms through the rational modeling from the SES, and then obtains the curvature and shape index of the molecular surface atoms.Using these parameters, we can identify the convex surfaces and concave surfaces.The results can be directly displayed on the SES model and colored according to shape index values, we can intuitively observe the protein-protein interaction sites and the shape of ligands binding to the protein.It provides the key clues to predicting the protein docking and new drugs research .