Recognition and architecture of the framework structure of protein

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(alpha), N(beta), and N(beta(alpha)beta) (the number of alpha-helices, beta-strands, and beta(alpha)beta 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 beta, alpha, and alpha/beta 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.