Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations

被引:61
作者
Perez, Alberto [1 ]
MacCallum, Justin L. [4 ]
Brini, Emiliano [1 ]
Simmerling, Carlos [1 ,2 ]
Dill, Ken A. [1 ,2 ,3 ]
机构
[1] SUNY Stony Brook, Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA
[2] SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA
[3] SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA
[4] Univ Calgary, Dept Chem, Calgary, AB T2N 1N4, Canada
基金
美国国家科学基金会;
关键词
MOLECULAR-DYNAMICS SIMULATIONS; HELIX-COIL TRANSITION; PARTICLE MESH EWALD; GENERALIZED BORN; ALPHA-HELIX; STATISTICAL POTENTIALS; PEPTIDE HELICES; BETA-HAIRPIN; MODEL; AMBER;
D O I
10.1021/acs.jctc.5b00662
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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 but 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 parametrized 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 + Gbnecla. Ff12SB-cMAP can be downloaded (https://github.com/laufercenter/Arnap.git) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments.
引用
收藏
页码:4770 / 4779
页数:10
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