Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm

BioData Min. 2018 Aug 8;11:17. doi: 10.1186/s13040-018-0176-6. eCollection 2018.

Abstract

Background: The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction process in order to reduce the prediction complexity.

Results: In this study, the ions motion optimization (IMO) algorithm was combined with the greedy algorithm (namely IMOG) and implemented to the HP model for the protein folding prediction based on the 2D-triangular-lattice model. Prediction results showed that the integration method IMOG provided a better prediction efficiency in a HP model. Compared to others, our proposed method turned out as superior in its prediction ability and resilience for most of the test sequences. The efficiency of the proposed method was verified by the prediction results. The global search capability and the ability to escape from the local best solution of IMO combined with a local search (greedy algorithm) to the new algorithm IMOG greatly improve the search for the best solution with reliable protein folding prediction.

Conclusion: Overall, the HP model integrated with IMO and a greedy algorithm as IMOG provides an improved way of protein structure prediction of high stability, high efficiency, and outstanding performance.

Keywords: Global search; Hydrophobic-polar (HP) model; IMOG; Ion motion optimization; Local search; Protein folding.