Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.
Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.
复制标题
基于网格的主链校正对隐式溶剂模拟的FF12SB蛋白力场。
DOI：
10.1021/acs.jctc.5b00662
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发表时间：
2015-10-13
影响因子：
5.5
通讯作者：
Dill KA
中科院分区：
文献类型：
--
作者：
Perez A;MacCallum JL;Brini E;Simmerling C;Dill KA
力场，如Amber的ff 12 SB，可以相当准确地模拟蛋白质和其他生物分子中的物理力。当与精确的溶剂化模型相结合时，力场能够洞察这些生物分子的构象偏好，转变，途径和自由能。当计算速度/成本问题时，通常使用隐式溶剂-以精度为代价。我们提出了一个经验性的网格状校正项-在cMAP的精神-的ff 12 SB蛋白质力场和GBneck 2隐式溶剂模型的组合。根据实验螺旋度数据对Ff 12 SB-cMAP进行参数化。我们提供了一组肽和蛋白质的验证。Ff 12 SB-cMAP成功地改善了在ff 12 SB + Gbneck 2中观察到的二级结构偏差。Ff 12 SB-cMAP可以下载（https：//github.com/laufercenter/Amap.git）并在Amber包中使用。它可以提高力场+隐式溶剂与实验的一致性。
Force fields, such as Amber’s ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways and free energies for these biomolecules. When computational speed/cost matters implicit solvent is often used -- at the cost of accuracy. We present an empirical grid-like correction term –in the spirit of cMAPs-- to the combination of the ff12SB protein force field and the GBneck2 implicit solvent model. Ff12SB-cMAP is parameterized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB+Gbneck2. Ff12SB-cMAP can be downloaded (https://github.com/laufercenter/Amap.git) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments.