Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction

Ab initio protein tertiary structure prediction is one of the long-standing problems in structural bioinformatics. With the help of the residue-residue contact and secondary structure prediction information, the accuracy of ab initio structure prediction can be enhanced. In this study, an improved differential evolution using the secondary structure and residue-residue contact information referred to as SCDE is proposed for protein structure prediction. In SCDE, two score models based on the secondary structure and contact information are proposed, and two selection strategies, namely, secondary structure-based selection strategy and contact-based selection strategy, are designed to guide conformation space search. In addition, a probability distribution function is designed to balance these two selection strategies. Experimental results on a benchmark dataset with 28 proteins and 4 free model targets in CASP12 demonstrate that the proposed SCDE is effective and efficient.