A Computational Method for Viewing Molecular Interactions in Docking

A huge amount of molecular data is available in protein data bank and various other libraries and this amount is increasing day by day. Devising new and efficient computational methods to extract useful information from this data is a big challenge for the researchers working in the field. Computational molecular docking refers to computational methods which attempt to obtain the best binding conformation of two interacting molecules. Information of the best binding conformation is useful in many applications such as rational drug design, recognition, cellular pathways, macromolecular assemblies, protein folding etc. Docking has three important aspects: (i) modeling of molecular shape, (ii) shape matching and (iii) scoring and ranking of potential solutions. In this paper, a new approach is proposed for shape matching in rigid body docking. The method gives visual information about the matching conformations of the molecules. In the approach proposed here, B-spline surface representation technique is used to model the patches of molecular surface. Surface normal and curvature properties are used to match these patches with each other. The 2-D approach used here for generation of surface patches is useful to pixellisation paradigm.