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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-12-01
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| Series: | Data in Brief |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340921008933 |
| _version_ | 1798026802721980416 |
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| author | Daniel Markthaler Niels Hansen |
| author_facet | Daniel Markthaler Niels Hansen |
| author_sort | Daniel Markthaler |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T18:41:11Z |
| format | Article |
| id | doaj.art-cec686fb64e8498b98425b4aa853f1ce |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-04-11T18:41:11Z |
| publishDate | 2021-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-cec686fb64e8498b98425b4aa853f1ce2022-12-22T04:08:58ZengElsevierData in Brief2352-34092021-12-0139107618Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase BDaniel Markthaler0Niels Hansen1University of Stuttgart, Institute of Thermodynamics and Thermal Process Engineering, Pfaffenwaldring 9, Stuttgart D-70569, GermanyCorresponding author.; University of Stuttgart, Institute of Thermodynamics and Thermal Process Engineering, Pfaffenwaldring 9, Stuttgart D-70569, GermanyThe 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.http://www.sciencedirect.com/science/article/pii/S2352340921008933MD simulationGROMACSUmbrella samplingMethanolCALB |
| spellingShingle | Daniel Markthaler Niels Hansen Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B Data in Brief MD simulation GROMACS Umbrella sampling Methanol CALB |
| 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 | MD simulation GROMACS Umbrella sampling Methanol CALB |
| url | http://www.sciencedirect.com/science/article/pii/S2352340921008933 |
| work_keys_str_mv | AT danielmarkthaler umbrellasamplinganddoubledecouplingdataformethanolbindingtocandidaantarcticalipaseb AT nielshansen umbrellasamplinganddoubledecouplingdataformethanolbindingtocandidaantarcticalipaseb |