Solving the Protein Folding Problem with a Bicriterion Genetic Algorithm on the Grid

Abstract

The exploration of potential multidimensional surfaces in protein folding is a non-trivial problem of extreme importance in computational biology. An evolutionary bicriterion grid-enabled protein folding approach is reported, classical molecular mechanics equations being employed for modeling inter-atomic interactions. Afferent computations were distributed on a nation-wide grid - GRID5000. A layered software design composed of dedicated frameworks is adopted due to the highly complex aspects inherent for the underlying volatile and dynamic execution environment. A brief insight on the existing approaches and the mathematical basis describing physical molecular interactions is offered, including derived semi-empirical and purely-empirical models. Introductory multicriterion formalisms enclosing the exposed approach are also presented