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Finding multiple reaction pathways via global optimization of action

Cited 28 time in Web of Science Cited 30 time in Scopus
Authors

Lee, Ju Yong; Lee, In Ho; Joung, In Suk; Lee, Joo Young; Brooks, Bernard R.

Issue Date
2017-05
Publisher
Nature Publishing Group
Citation
Nature Communications, Vol.8, p. 15443
Abstract
Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barriers via crossovers and mutations of pathways and finds all possible pathways of small systems without initial guesses on pathways. The rank order and the transition time distribution of multiple pathways are in good agreement with those of long Langevin dynamics simulations. The lowest action folding pathway of FSD-1 is consistent with recent experiments. The results show that Action-CSA is an efficient and robust computational approach to study the multiple pathways of complex reactions and large-scale conformational changes.
URI
https://hdl.handle.net/10371/201525
DOI
https://doi.org/10.1038/ncomms15443
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  • Graduate School of Convergence Science & Technology
  • Dept. of Molecular and Biopharmaceutical Sciences
Research Area AI models for drug discovery, Free energy calculation, Molecular dynamics, 분자동역학, 신약개발을 위한 AI 모델, 자유에너지 계산

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