Protein functional-group 3D motif and its applications

作     者：Yuzhen Ye Tao Xie Dafu Ding 

作者机构：Chinese Acad Sci Shanghai Inst Biochem Shanghai 200031 Peoples R China 

出 版 物：《Chinese Science Bulletin》 (Chin. Sci. Bull.)

年 卷 期：2000年第45卷第22期

页      面：2044-2052页

核心收录：

学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 

基　　金：National High Technology "863" Programs of China, (863-103-03-03) Shanghai Key Program of Basic Research National Natural Science Foundation of China, NSFC, (39990600-03) 

主　　题：functional-group 3D motif RMSD of distance matrix random probability expectation functional prediction. 

摘      要：Representing and recognizing protein active sites sequence motif (1D motif) and structural motif (3D motif) is an important topic for predicting and designing protein function. Prevalent methods for extracting and searching 3D motif always consider residue as the minimal unit, which have limited sensitivity. Here we present a new spatial representation of protein active sites, called functional-group 3D motif , based on the fact that the functional groups inside a residue contribute mostly to its function. Relevant algorithm and computer program are developed, which could be widely used in the function prediction and the study of structural-function relationship of proteins. As a test, we defined a functional-group 3D motif of the catalytic triad and oxyanion hole with the structure of porcine trypsin (PDB code: 1mct) as the template. With our motif-searching program, we successfully found similar sub-structures in trypsins, subtilisins and α/β hydrolases, which show distinct folds but share