A1 Refereed original research article in a scientific journal
Efficient Amino Acid Conformer Search with Bayesian Optimization
Authors: Fang L, Makkonen E, Todorovic M, Rinke P, Chen X
Publisher: AMER CHEMICAL SOC
Publication year: 2021
Journal: Journal of Chemical Theory and Computation
Journal name in source: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Journal acronym: J CHEM THEORY COMPUT
Volume: 17
Issue: 3
First page : 1955
Last page: 1966
Number of pages: 12
ISSN: 1549-9618
DOI: https://doi.org/10.1021/acs.jctc.0c00648
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.
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.
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