3D image and graph based Computation of Protein Surface

Abstract

Abstract The accessible surface of a macromolecule is a significant determinant of its action. The interaction between biomolecules or protein-ligand is dependent on their surfaces rather than their bulk properties. Identifying these local properties of bimolecular surfaces plays a vital role in the area of biomedicine. For example, identifying binding sites, docking etc. In this paper we describe an algorithm for computing the molecular surface of protein. The algorithm considers the 3D structure of the protein as a 3D image. The algorithm constructs a 3D graph corresponding to the size of 3D image data volume; the graph nodes correspond to image voxels.The idea is drawn from the cost minimization in a graph developed by Thedens and Fleagle[1]. The algorithm uses a Dynamic Programming Technique to avoid combinatorial explosion of the legal local surface.