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...

Description complète

Enregistré dans:

Détails bibliographiques
Auteurs principaux:	Daniel Markthaler, Niels Hansen
Format:	article
Langue:	EN
Publié:	Elsevier 2021
Sujets:	MD simulation GROMACS Umbrella sampling Methanol CALB Computer applications to medicine. Medical informatics R858-859.7 Science (General) Q1-390
Accès en ligne:	https://doaj.org/article/cec686fb64e8498b98425b4aa853f1ce
Tags:	Ajouter un tag Pas de tags, Soyez le premier à ajouter un tag!

id	oai:doaj.org-article:cec686fb64e8498b98425b4aa853f1ce
record_format	dspace
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
_version_	1718408345580208128

Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B

Documents similaires