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...

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Autores principales: Daniel Markthaler, Niels Hansen
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Publicado: Elsevier 2021
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spelling oai:doaj.org-article:cec686fb64e8498b98425b4aa853f1ce2021-11-28T04:33:23ZUmbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B2352-340910.1016/j.dib.2021.107618https://doaj.org/article/cec686fb64e8498b98425b4aa853f1ce2021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2352340921008933https://doaj.org/toc/2352-3409The 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.Daniel MarkthalerNiels HansenElsevierarticleMD simulationGROMACSUmbrella samplingMethanolCALBComputer applications to medicine. Medical informaticsR858-859.7Science (General)Q1-390ENData in Brief, Vol 39, Iss , Pp 107618- (2021)
institution DOAJ
collection DOAJ
language EN
topic MD simulation
GROMACS
Umbrella sampling
Methanol
CALB
Computer applications to medicine. Medical informatics
R858-859.7
Science (General)
Q1-390
spellingShingle MD simulation
GROMACS
Umbrella sampling
Methanol
CALB
Computer applications to medicine. Medical informatics
R858-859.7
Science (General)
Q1-390
Daniel Markthaler
Niels Hansen
Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B
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 article
author Daniel Markthaler
Niels Hansen
author_facet Daniel Markthaler
Niels Hansen
author_sort Daniel Markthaler
title 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_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_sort umbrella sampling and double decoupling data for methanol binding to candida antarctica lipase b
publisher Elsevier
publishDate 2021
url https://doaj.org/article/cec686fb64e8498b98425b4aa853f1ce
work_keys_str_mv AT danielmarkthaler umbrellasamplinganddoubledecouplingdataformethanolbindingtocandidaantarcticalipaseb
AT nielshansen umbrellasamplinganddoubledecouplingdataformethanolbindingtocandidaantarcticalipaseb
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