Sequence-based protein structure optimization using enhanced simulated annealing algorithm on a coarse-grained model
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ORIGINAL PAPER
Sequence-based protein structure optimization using enhanced simulated annealing algorithm on a coarse-grained model Lizhong Zhang 1,2 & He Ma 1,3 & Wei Qian 4 & Haiyan Li 5 Received: 9 October 2019 / Accepted: 30 July 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The understanding of protein structure is vital to determine biological function. We presented an enhanced simulated annealing (ESA) algorithm to investigate protein three-dimensional (3D) structure on a coarse-grained model. Inside the algorithm, we adjusted exploration equations to achieve good search intensity. To that end, our algorithm used (i) a multivariable disturbance operator for diversification of solution, (ii) a sign function to improve randomness of solution, and (iii) taking remainder operation performed on floating-point number to tackle out-of-range solution. By monitoring energy value throughout the simulation, the energy-optimal state can be found. The ESA algorithm was tested on artificial and real protein sequences with different lengths. The results show that our algorithm outperforms conventional simulated annealing algorithm and can compete with the reported algorithms before. Especially, our algorithm can obtain folding conformations with specific structural features. Further analysis shows that simulating trajectory of seeking the lowest energy can exhibit thermodynamic behavior of protein folding. Keywords Protein structure . Off-lattice model . Neighborhood solution . Thermodynamic behavior
Introduction Determination of protein three-dimensional (3D) structure provides very important information in biology researches, especially for understanding protein functions and drug design
[1]. At present, there are two dominant technologies, experimental and computational approaches, to solve protein structure prediction problem. The experimental methods mainly involve X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (Cryo-
Highlights • A multivariable disturbance operator for diversification of neighborhood solution. • Taking remainder operation performed on floating-point number to tackle out-of-range solution. • The algorithm can obtain folding conformations with specific structural features. • The simulating trajectory of seeking low energy can reflect thermodynamic behavior of protein folding. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00894-020-04490-6) contains supplementary material, which is available to authorized users. * He Ma [email protected] 1
College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
2
College of Computer Science and Technology, Shenyang University of Chemical Technology, Shenyang 110142, China
3
Key Laboratory of Medical Image Computing, Ministry of Education, Northeastern University, Shenyang 110169, China
4
Department of Electrical and Computer Engineering, College of Engineering, University of
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