MIAX: A Nobel System for Assessment of Macromolecular Interaction in Cond ensed Phases.
1) Description of the Interaction Model and Simulation Algorithm

Carlos Adriel Del Carpio Munoz (carlos@transless.eco.tut.ac.jp)
Atsushi Yoshimori (yosimori@translell.eco.tut.ac.jp)

Department of Ecologocal Engineering, Toyohashi University of Technology, Tempaku
Toyohashi 441-8580, Japan


Abstract

We describe a nobel computer system directed to evaluate protein complex formation in a liquid environment. The relevant feature of the system is a potential function expressing the main thermodynamic and kinetic factors leading to protein interaction in solution. The protein interaction model express the interaction energy as basically composed of three forces: electrostatic(hydrogen bond), van der Waals, and hydrophobic. The latter is defined in function of the forces between the monomers and the solvent.

The interaction model implemented in the system has proven a high discrimination ability between different protein dockings, scoring high those close to the observed crystal structures. These results have led to the establishment of the basic principles underlying protein interaction, which constitutes the main way of expression of the biological function of these macromolecules.

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Japanese Society for Bioinformatics