Efficient Amino Acid Conformer Search with Bayesian Optimization
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A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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Date
2021-03-09
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en
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12
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Journal of Chemical Theory and Computation, Volume 17, issue 3, pp. 1955–1966
Abstract
Finding low-energy molecular conformers is challenging due to the high dimensionality of the search space and the computational cost of accurate quantum chemical methods for determining conformer structures and energies. Here, we combine active-learning Bayesian optimization (BO) algorithms with quantum chemistry methods to address this challenge. Using cysteine as an example, we show that our procedure is both efficient and accurate. After only 1000 single-point calculations and approximately 80 structure relaxations, which is less than 10% computational cost of the current fastest method, we have found the low-energy conformers in good agreement with experimental measurements and reference calculations. To test the transferability of our method, we also repeated the conformer search of serine, tryptophan, and aspartic acid. The results agree well with previous conformer search studies.Description
Funding Information: This work was supported by the Academy of Finland (project numbers 308647, 314298, and 316601) and through their Flagship program: Finnish Center for Artificial Intelligence FCAI. We thank CSC, the Finnish IT Center for Science, and Aalto Science IT for computational resources. This work is supported by COST (European Cooperation in Science and Technology) Action 18234. L.F. thanks Guoxu Zhang, Marc Dvorak, Jingrui Li, and Annika Stuke for the help with FHI-Aims. He also acknowledges financial support from the Chinese Scholarship Council (grant no. [2017]3109). 1 Publisher Copyright: © 2020 American Chemical Society. All rights reserved. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.
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Fang, L, Makkonen, E, Todorović, M, Rinke, P & Chen, X 2021, ' Efficient Amino Acid Conformer Search with Bayesian Optimization ', Journal of Chemical Theory and Computation, vol. 17, no. 3, pp. 1955–1966 . https://doi.org/10.1021/acs.jctc.0c00648