Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces

Authors:
Satoshi Koizumi;Keisuke Imada;Tomonobu Ozaki;Takenao Ohkawa
Affiliations:
Graduate School of Engineering, Kobe University,;Graduate School of Science and Technology, Kobe University,;Organization of Advanced Science and Technology, Kobe University,;Graduate School of Engineering, Kobe University,
Venue:
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Year:
2008

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Abstract

There is much research on the automatic extraction of new binding sites in proteins by searching for common sites in proteins with identical functions. While many binding sites consist of concave structures, it is difficult to compare such concaves directly due to the various sizes of concaves. To cope with this difficulty and to realize detailed and precise comparisons between concaves, we propose a method of searching for and comparing concaves by gradually changing the size. By experiments with enzyme proteins, we confirmed that extraction accuracy for the binding sites is improved.