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甲醇与脂肪酶B结合的伞形采样和双重去耦数据。

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

作者信息

Markthaler Daniel, Hansen Niels

机构信息

University of Stuttgart, Institute of Thermodynamics and Thermal Process Engineering, Pfaffenwaldring 9, Stuttgart D-70569, Germany.

出版信息

Data Brief. 2021 Nov 22;39:107618. doi: 10.1016/j.dib.2021.107618. eCollection 2021 Dec.

Abstract

The binding free-energy profile of methanol to 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.

摘要

使用OPLS全原子力场,通过伞形采样分子动力学模拟,计算了甲醇在无限稀释和甲醇浓度为6.1 M时与脂肪酶B(CALB)的结合自由能分布。通过采用炼金术双去耦模拟对结果进行了额外验证。在一篇相关研究文章中,结合自由能分布被用于验证从直接计数模拟获得的自由能分布,目的是利用后者中编码的动力学信息。这项工作中提供的数据将有助于研究浓度对结合的影响、测试替代自由能方法或对相关系统使用所提出的模拟协议。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13be/8633857/de13a8b12e5a/gr1.jpg

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