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Int. J. Mol. Sci. 2015, 16(7), 15136-15149; doi:10.3390/ijms160715136

A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences

1
,
1,†,* and 2,†,*
1
Department of Computer Science and Information Engineering, National Chung Cheng University, Min-Hsiung Township, Chia-yi County 62102, Taiwan
2
Department of Information Engineering and Computer Science, Feng Chia University, Taichung 40724, Taiwan
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Salvador Ventura
Received: 28 March 2015 / Revised: 25 June 2015 / Accepted: 25 June 2015 / Published: 3 July 2015
(This article belongs to the Collection Protein Folding)
View Full-Text   |   Download PDF [1481 KB, uploaded 3 July 2015]   |  

Abstract

Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP. View Full-Text
Keywords: backbone angle preferences; protein structure; multiobjective optimization; face-centered cubic backbone angle preferences; protein structure; multiobjective optimization; face-centered cubic
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Tsay, J.-J.; Su, S.-C.; Yu, C.-S. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences. Int. J. Mol. Sci. 2015, 16, 15136-15149.

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