MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction

Abstract

MotivationThe mathematically optimal solution in computational protein folding simulations does not always correspond to the native structure, due to the imperfection of the energy force fields. There is therefore a need to search for more diverse suboptimal solutions in order to identify the states close to the native. We propose a novel multimodal optimization protocol to improve the conformation sampling efficiency and modeling accuracy of de novo protein structure folding simulations. ResultsA distance-assisted multimodal optimization sampling algorithm, MMpred, is proposed for de novo protein structure prediction. The protocol consists of three stages: The first is a modal exploration stage, in which a structural similarity evaluation model DMscore is designed to control the diversity of conformations, generating a population of diverse structures in different low-energy basins. The second is a modal maintaining stage, where an adaptive clustering algorithm MNDcluster is proposed to divide the populations and merge the modal by adjusting the annealing temperature to locate the promising basins. In the last stage of modal exploitation, a greedy search strategy is used to accelerate the convergence of the modal. Distance constraint information is used to construct the conformation scoring model to guide sampling. MMpred is tested on a large set of 320 non-redundant proteins, where MMpred obtains models with TM-score[≥]0.5 on 268 cases, which is 20.3% higher than that of Rosetta guided with the same set of distance constraints. The results showed that MMpred can help significantly improve the model accuracy of protein assembly simulations through the sampling of multiple promising energy basins with enhanced structural diversity. AvailabilityThe source code and executable versions are freely available at https://github.com/iobio-zjut/MMpred. Contactzgj@zjut.edu.cn or zhng@umich.edu or sujz@wmu.edu.cn