Analysis of geometrical and topological aptitude for protein-protein interaction

Protein-protein interaction takes usually place on an extended area of the external molecules surfaces that are morphologically fitting. Geometric and topological congruence (i.e. concavity and convexity correspondences) is required to support the neighboring interaction of surface patches belonging to the two protein molecules. It is therefore important to adopt representations and data structures that can facilitate the analysis and the implementation of techniques for the evaluation of geometric and topological properties on extended surfaces. These areas of activity are usually roughly “planar” but with local concavity and complexity that must match each other for interacting. To this purpose we are suggesting a solution different from the one of ligand-protein interaction in which are involved a pocket and a small molecule. The solution here suggested is based on the concavity tree representation. Starting from the convex hull of the protein molecule a recursive process leads to a series of concavity and meta-concavity that allows reaching the detail level required. The consequence of the recursive process is obviously a hierarchical data structure (a tree) which at each level supports a complete description of a surface. Each node of the tree contains an array of features that support the geometrical, topological and biochemical properties of the correspondent surface patch