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Efficient Amino Acid Conformer Search with Bayesian Optimization
[Image: see text] 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) a...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023666/ https://www.ncbi.nlm.nih.gov/pubmed/33577313 http://dx.doi.org/10.1021/acs.jctc.0c00648 |
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author | Fang, Lincan Makkonen, Esko Todorović, Milica Rinke, Patrick Chen, Xi |
author_facet | Fang, Lincan Makkonen, Esko Todorović, Milica Rinke, Patrick Chen, Xi |
author_sort | Fang, Lincan |
collection | PubMed |
description | [Image: see text] 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. |
format | Online Article Text |
id | pubmed-8023666 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-80236662021-04-07 Efficient Amino Acid Conformer Search with Bayesian Optimization Fang, Lincan Makkonen, Esko Todorović, Milica Rinke, Patrick Chen, Xi J Chem Theory Comput [Image: see text] 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. American Chemical Society 2021-02-12 2021-03-09 /pmc/articles/PMC8023666/ /pubmed/33577313 http://dx.doi.org/10.1021/acs.jctc.0c00648 Text en © 2021 American Chemical Society Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Fang, Lincan Makkonen, Esko Todorović, Milica Rinke, Patrick Chen, Xi Efficient Amino Acid Conformer Search with Bayesian Optimization |
title | Efficient Amino Acid Conformer Search with Bayesian
Optimization |
title_full | Efficient Amino Acid Conformer Search with Bayesian
Optimization |
title_fullStr | Efficient Amino Acid Conformer Search with Bayesian
Optimization |
title_full_unstemmed | Efficient Amino Acid Conformer Search with Bayesian
Optimization |
title_short | Efficient Amino Acid Conformer Search with Bayesian
Optimization |
title_sort | efficient amino acid conformer search with bayesian
optimization |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023666/ https://www.ncbi.nlm.nih.gov/pubmed/33577313 http://dx.doi.org/10.1021/acs.jctc.0c00648 |
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