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Parallel genetic algorithms on PARAM for conformation of biopolymers

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2 Author(s)
V. Sundararajan ; Applications Group, Centre for Dev. of Adv. Comput., Pune, India ; A. S. Kolaskar

A software is developed using genetic algorithms to predict the structure of a polypeptide chain. The algorithm is based on the principle of evolution and it improves the solution of the posed problem by genetic operations crossovers and mutations. Dihedral angles (φ,ψ) are taken as the basic variables for the structure of the molecules and genetic operations are carried over on a population of binary strings of (φ,ψ) angles. First, a sequential code is developed in FORTRAN on a standard workstation. A parallel version of the program is implemented on a distributed computing platform PARAM, developed by CDAC. The methodology and the practical aspects of the algorithm is presented with case studies of a dipeptide and an octapeptide. The usefulness of the migration model, developed for the first time, in achieving efficiency is stressed. The migration model proved to be more efficient and the minimisation for the octapeptide improved from 2% to 10%. This improvement is expected to be more pronounced for larger molecules

Published in:

High Performance Computing, 1996. Proceedings. 3rd International Conference on

Date of Conference:

19-22 Dec 1996