Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme

• Published in: Journal of computer-aided molecular design 2004-12, Vol.18 (12), p.797-810
• Main Authors: Zhang, Guang-Zheng, Huang, De-Shuang
• Format: Article
• Language: English
• Subjects: Algorithms; Binding Sites; Computer Simulation; Models, Molecular; Neural networks; Neural Networks (Computer); Protein Folding; Proteins - chemistry; Residues; Studies
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-005-0578-7

Inter-residue contacts map prediction is one of the most important intermediate steps to the protein folding problem. In this paper, we focus on the problem of protein inter-residue contacts map prediction based on neural network technique. Firstly, we use a genetic algorithm (GA) to optimize the radial basis function widths and hidden centers of a radial basis function neural network (RBFNN), then a novel binary encoding scheme is employed to train the network for the purpose of learning and predicting the inter-residue contacts patterns of protein sequences got from the protein data bank (PDB). The experimental evidence indicates the utility of our proposed encoding strategy and GA optimized RBFNN. Moreover, the simulation results demonstrate that the network got a better performance for these proteins, whose residue length falls into the area of (100, 300), and the predicted accuracy with a contact threshold of 7 Angstroms scores higher than the other 3 values with 5, 6, and 8 Angstroms.