Abstract
3D structure pf proteins deeply takes part in the expression of the protein that is an important composition element of the living thing. The molecular surface of the protein have very complex shapes, and contains a lot of projections and the hollow shapes (Hereafter, it is called ruggedness shapes).It is well-known that the function of the protein appears strongly in that bumpy part. We propose a technique to extract local bumpy shapes from molecular surface geometry database (eF-site), and classify them based on their geometry. Moreover, we propose an interface for effectively visualizing the result of extraction and classification of the local bumpy shapes.This technique assumes that molecule surface is approximated as a triangular mesh.It first extracts groups of triangles forming local bumpy parts. It then calculates feature values and forms a histogram for each bumpy parts, that denotes the distribution of distances of points on the bunpy parts around the axis. It finally clusters the bumpy parts according to the histogram. We use the hierarchical data technique "Heiankyo view" as a visual interface to explore the clustering results. Our technique is one of the fundamental step for the analysis of partial similarity of the molecular surface among proteins.
