MO4: A Many-Objective Evolutionary Algorithm for Protein Structure Prediction

Zhenyu Lei, Shangce Gao, Zhiming Zhang, Mengchu Zhou, Jiujun Cheng

Research output: Contribution to journalArticlepeer-review

56 Scopus citations


Protein structure prediction (PSP) problems are a major biocomputing challenge, owing to its scientific intrinsic that assists researchers to understand the relationship between amino acid sequences and protein structures, and to study the function of proteins. Although computational resources increased substantially over the last decade, a complete solution to PSP problems by computational methods has not yet been obtained. Using only one energy function is insufficient to characterize proteins because of their complexity. Diverse protein energy functions and evolutionary computation algorithms have been extensively studied to assist in the prediction of protein structures in different ways. Such algorithms are able to provide a better protein with less computational resources requirement than deep learning methods. For the first time, this study proposes a many-objective PSP (MaOPSP) problem with four types of objectives to alleviate the impact of imprecise energy functions for predicting protein structures. A many-objective evolutionary algorithm (MaOEA) is utilized to solve MaOPSP. The proposed method is compared with existing methods by examining 34 proteins. An analysis of the objectives demonstrates that our generated conformations are more reasonable than those generated by single/multiobjective optimization methods. Experimental results indicate that solving a PSP problem as an MaOPSP problem with four objectives yields better PSPs, in terms of both accuracy and efficiency. The source code of the proposed method can be found at

Original languageEnglish (US)
Pages (from-to)417-430
Number of pages14
JournalIEEE Transactions on Evolutionary Computation
Issue number3
StatePublished - Jun 1 2022

All Science Journal Classification (ASJC) codes

  • Software
  • Theoretical Computer Science
  • Computational Theory and Mathematics


  • Deep learning
  • evolutionary computation
  • free modeling
  • many-objective optimization evolutionary algorithm (MaOEA)
  • protein structure prediction (PSP)


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