Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces
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.
KeywordsFunctional Site Molecular Surface Surface Data Neighboring Vertex Test Protein
- 3.Shrestha, N.L., Kawaguchi, Y., Nakagawa, T., Ohkawa, T.: A method of filtering protein surface motifs based on similarity among local surfaces (2004)Google Scholar
- 6.Stryer, L.: Biochemistry, Tokyou Kagaku DoujinGoogle Scholar
- 9.Takagi, M., Shimoda, H.: Handbook of image analysis. Tokyo University Publication (1991)Google Scholar
- 10.Murzina, A.G., Brennera, S.E., Hubbarda, T., Chothia, C.: Scop: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536–540 (2004)Google Scholar