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Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B
The binding free-energy profile of methanol to Candida antarctica lipase B (CALB) was calculated at infinite dilution and at a finite methanol concentration of 6.1 M using umbrella sampling molecular dynamics simulations with the OPLS all-atom force field. An additional validation of the results was...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8633857/ https://www.ncbi.nlm.nih.gov/pubmed/34877385 http://dx.doi.org/10.1016/j.dib.2021.107618 |
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author | Markthaler, Daniel Hansen, Niels |
author_facet | Markthaler, Daniel Hansen, Niels |
author_sort | Markthaler, Daniel |
collection | PubMed |
description | The binding free-energy profile of methanol to Candida antarctica lipase B (CALB) was calculated at infinite dilution and at a finite methanol concentration of 6.1 M using umbrella sampling molecular dynamics simulations with the OPLS all-atom force field. An additional validation of the results was performed by employing alchemical double decoupling simulations. The binding free-energy profiles have been used in a related research article to validate free-energy profiles obtained from direct counting simulations with the aim to use the kinetic information encoded in the latter. The data provided in this work will be useful to study concentration effects on binding, to test alternative free energy methods or to use the proposed simulation protocol for related systems. |
format | Online Article Text |
id | pubmed-8633857 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-86338572021-12-06 Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B Markthaler, Daniel Hansen, Niels Data Brief Data Article The binding free-energy profile of methanol to Candida antarctica lipase B (CALB) was calculated at infinite dilution and at a finite methanol concentration of 6.1 M using umbrella sampling molecular dynamics simulations with the OPLS all-atom force field. An additional validation of the results was performed by employing alchemical double decoupling simulations. The binding free-energy profiles have been used in a related research article to validate free-energy profiles obtained from direct counting simulations with the aim to use the kinetic information encoded in the latter. The data provided in this work will be useful to study concentration effects on binding, to test alternative free energy methods or to use the proposed simulation protocol for related systems. Elsevier 2021-11-22 /pmc/articles/PMC8633857/ /pubmed/34877385 http://dx.doi.org/10.1016/j.dib.2021.107618 Text en © 2021 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Data Article Markthaler, Daniel Hansen, Niels Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B |
title | Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B |
title_full | Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B |
title_fullStr | Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B |
title_full_unstemmed | Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B |
title_short | Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B |
title_sort | umbrella sampling and double decoupling data for methanol binding to candida antarctica lipase b |
topic | Data Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8633857/ https://www.ncbi.nlm.nih.gov/pubmed/34877385 http://dx.doi.org/10.1016/j.dib.2021.107618 |
work_keys_str_mv | AT markthalerdaniel umbrellasamplinganddoubledecouplingdataformethanolbindingtocandidaantarcticalipaseb AT hansenniels umbrellasamplinganddoubledecouplingdataformethanolbindingtocandidaantarcticalipaseb |