Research on predicting 2D-HP protein folding using reinforcement learning with full state space

Abstract

Abstract Background Protein structure prediction has always been an important issue in bioinformatics. Prediction of the two-dimensional structure of proteins based on the hydrophobic polarity model is a typical non-deterministic polynomial hard problem. Currently reported hydrophobic polarity model optimization methods, greedy method, brute-force method, and genetic algorithm usually cannot converge robustly to the lowest energy conformations. Reinforcement learning with the advantages of continuous Markov optimal decision-making and maximizing global cumulative return is especially suitable for solving global optimization problems of biological sequences. Results In this study, we proposed a novel hydrophobic polarity model optimization method derived from reinforcement learning which structured the full state space, and designed an energy-based reward function and a rigid overlap detection rule. To validate the performance, sixteen sequences were selected from the classical data set. The results indicated that reinforcement learning with full states successfully converged to the lowest energy conformations against all sequences, while the reinforcement learning with partial states folded 50% sequences to the lowest energy conformations. Reinforcement learning with full states hits the lowest energy on an average 5 times, which is 40 and 100% higher than the three and zero hit by the greedy algorithm and reinforcement learning with partial states respectively in the last 100 episodes. Conclusions Our results indicate that reinforcement learning with full states is a powerful method for predicting two-dimensional hydrophobic-polarity protein structure. It has obvious competitive advantages compared with greedy algorithm and reinforcement learning with partial states.

Keywords

• Reinforcement learning
• HP model
• Structure prediction