Generic parallel genetic algorithm framework for protein optimisation

Abstract

Proteins are one of the most vital macromolecules on the cellular level. In order to understand the function of a protein, its structure needs to be determined. For this purpose, different computational approaches have been introduced. Genetic algorithms can be used to search the vast space of all possible conformations of a protein in order to find its native structure. A framework for design of such algorithms that is both generic, easy to use and performs fast on distributed systems may help further development of genetic algorithm based approaches. We propose such a framework based on a parallel master-slave model which is implemented in C++ and Message Passing Interface. We evaluated its performance on distributed systems with a different number of processors and achieved a linear acceleration in proportion to the number of processing units. © 2011 Springer-Verlag.