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Recognition and architecture of the framework structure of protein
Author(s) -
Luo Liaofu,
Li Xiaoqin
Publication year - 2000
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(20000401)39:1<9::aid-prot2>3.0.co;2-c
Subject(s) - alpha (finance) , test set , beta (programming language) , set (abstract data type) , protein secondary structure , universality (dynamical systems) , sequence (biology) , mathematics , computer science , algorithm , artificial intelligence , theoretical computer science , biology , physics , statistics , programming language , biochemistry , genetics , construct validity , quantum mechanics , psychometrics
Based on the concept that the framework structure of a protein is determined by its secondary structure sequence, a new method for recognition and prediction of the structural class is suggested. By use of parameters N α , N β , and N βαβ (the number of α‐helices, β‐strands, and βαβ fragments), one can recognize the structural class with an accuracy higher than 90% when applied to the complete set (standard set) published in October 1995 and the structure data newly released before July 1998 (test set). Furthermore, the framework structures of β, α, and α/β protein are studied. It is found that these structures can be built from some basic units and that their architecture obeys some definite rules. Based on the packing of these basic units a set of rules for the recognition of topologies of the framework structure are worked out. When applied to the 1995 standard set and the 1998 test set the rates of correct recognition are higher than 77%. The simplicity and universality of framework structures are indicated which may be related to the evolutionary conservation of these folds. Proteins 2000;39:9–25. © 2000 Wiley‐Liss, Inc.