Differential evolution for protein folding optimization based on a three-dimensional AB off-lattice model

  • Borko BoškovićEmail author
  • Janez Brest
Original Paper


This paper presents a differential evolution algorithm that is adapted for the protein folding optimization on a three-dimensional AB off-lattice model. The proposed algorithm is based on a self-adaptive differential evolution that improves the algorithm efficiency and reduces the number of control parameters. A mutation strategy for the fast convergence is used inside the algorithm. A temporal locality is used in order to speed up the algorithm convergence additionally and to find amino-acid conformations with the lowest free energy values. Within this mechanism a new vector is calculated when the trial vector is better than the corresponding vector from the population. This new vector is likely better than the trial vector and this accelerates convergence speed. Because of the fast convergence the algorithm has some chance to be trapped into the local optima. To mitigate this problem the algorithm includes reinitialization. The proposed algorithm was tested on amino-acid sequences that are used frequently in literature. The obtained results show that the proposed algorithm is superior to the algorithms from the literature and the obtained amino-acid sequences have significantly lower free energy values.

Graphical Abstract

Protein folding optimization on a three-dimensional AB off-lattice model using the differential evolution algorithm.


Differential evolution Three-dimensional AB off-lattice model Protein folding optimization 



Our work was supported by the Slovenian Research Agency under Program P2-0041 (Computer Systems, Methodologies, and Intelligent Services).

Supplementary material

Folding simulation for 1AGT (AVI 2.50 MB)

Folding simulation for 2EWH (AVI 9.04 MB)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Faculty of Electrical Engineering and Computer ScienceUniversity of MariborMariborSlovenia

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