MIAX: A System for Assessment of Macromolecular Interaction. 4) Interaction Site Inference by Molecular Hydrophobic and Electrostatic Analysis

Specific recognition of the interaction site in protein-protein interactions is the most relevant requirement to predict biochemical function of proteins. The role played by electrophysical complementarity as a determinant of protein-protein interaction is important. In the present study we have focused on the distribution of these forces on the protein surface. the distribution is evaluated by means of a self organizing map (SOM) [5] which renders a nonlinear projection of the high dimensional configuration of the electrophysical forces on the surface of the monomers into a lower dimensional map of neurons. In the analysis of these map, we undertake the problem of reduction of the huge configuration search space for the complex in order to improve processing times of the system for automatic assessment of macromolecular interaction system (MIAX) [2, 3]. We evaluate the algorithm predicting plausible interaction sites for several complexes whose coordinates are found in the PDB,and comparing them with inferred candidate interaction regions.