Stochastic Fractal Search Algorithm for 3D Protein Structure Prediction

Abstract

Protein structure prediction (PSP) is a process to predict protein three-dimensional structures based on the known amino acid sequence, which has a very important significance for biological information research, disease treatment and drug research and development and so on. PSP is a typical NP problem: firstly, we should establish the appropriate mathematical model according to the problem; secondly, a solution process for the model was given based on an appropriate optimization algorithm. In this paper, an original protein structure prediction scheme is transformed into a numerical optimization problem by adopting AB off-lattice model. Then the minimum free energy value of protein structure will be gained by using Stochastic Fractal Search algorithm (SFS). Experiments show that the proposed method outperforms other algorithms on the accuracy of calculating the protein sequence energy value, which is turned out to be an effective way to analyze protein structure.