Incorporation of Solvent Effect into Multi-Objective Evolutionary Algorithm for Improved Protein Structure Prediction

Document Type

Article

Publication Date

7-1-2018

Abstract

The problem of predicting the three-dimensional (3-D) structure of a protein from its one-dimensional sequence has been called the 'holy grail of molecular biology', and it has become an important part of structural genomics projects. Despite the rapid developments in computer technology and computational intelligence, it remains challenging and fascinating. In this paper, to solve it we propose a multi-objective evolutionary algorithm. We decompose the protein energy function Chemistry at HARvard Macromolecular Mechanics force fields into bond and non-bond energies as the first and second objectives. Considering the effect of solvent, we innovatively adopt a solvent-accessible surface area as the third objective. We use 66 benchmark proteins to verify the proposed method and obtain better or competitive results in comparison with the existing methods. The results suggest the necessity to incorporate the effect of solvent into a multi-objective evolutionary algorithm to improve protein structure prediction in terms of accuracy and efficiency.

Identifier

85029187836 (Scopus)

Publication Title

IEEE ACM Transactions on Computational Biology and Bioinformatics

External Full Text Location

https://doi.org/10.1109/TCBB.2017.2705094

ISSN

15455963

PubMed ID

28534784

First Page

1365

Last Page

1378

Issue

4

Volume

15

Grant

17K12751

Fund Ref

Japan Society for the Promotion of Science

This document is currently not available here.

Share

COinS