A method of comparing protein molecular surface based on normal vectors with attributes and its application to function identification

Authors:
Yoshikazu Kaneta;Norimasa Shoji;Takenao Ohkawa;Haruki Nakamura
Affiliations:
Department of Multimedia Engineering, Graduate School of Information Science and Technology Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;Department of Multimedia Engineering, Graduate School of Information Science and Technology Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;Department of Multimedia Engineering, Graduate School of Information Science and Technology Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;Institute for Protein Research, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
Venue:
Information Sciences—Applications: An International Journal
Year:
2002

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Abstract

Recent researches have clarified that the function of protein depends on its molecular surface. They suggest the possibility of the protein function identification based on the molecular surface comparison, in which a molecular surface of an unknown protein is compared with many surfaces of known active sites as reference templates. This paper presents an effective surface comparison method by using normal vectors with attributes of the curvature and the physical properties on projections and depressions. The vectors that should be matched are limited by extracting two vectors at similar relative positions and with the attributes of surface in order to reduce computational complexity. The proposed method was applied to 11 surface data. As a result, the mean calculation time was about 3 min, and it was possible to compare at approximately an optimal location. This method was applied to 103 surface data. The result of identification showed 95.2% identification accuracy.