Protein Conformational Search Using Bees Algorithm

Abstract

Proteins perform many biological functions in the human body. The structure of the protein determines its function. In order to predict the protein structure computationally, protein must be represented in a proper representation. To this end, an energy function is used to calculate its energy and a conformational search algorithm is used to search the conformational search space to find the lowest free energy conformation. In this paper, the Bees Algorithm, i.e. a Swarm Intelligence based algorithm inspired by the foraging behaviour of honey bees colony, is adapted to search the protein conformational search space. The algorithm was able to find the lowest free energy conformation of Met-enkephaline using ECEPP/2 force fields.