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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2021
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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) |
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MD simulation GROMACS Umbrella sampling Methanol CALB Computer applications to medicine. Medical informatics R858-859.7 Science (General) Q1-390 |
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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 |
_version_ |
1718408345580208128 |