Journal article
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
The journal of physical chemistry. B, Vol.121(16), pp.4023-4039
04/27/2017
DOI: 10.1021/acs.jpcb.7b02320
PMID: 28306259
Abstract
The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.
Details
- Title: Subtitle
- Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
- Creators
- Lee-Ping Wang - University of California, DavisKeri A McKiernan - Stanford UniversityJoseph Gomes - Stanford UniversityKyle A Beauchamp - CounsylTeresa Head-Gordon - Lawrence Berkeley National LaboratoryJulia E Rice - IBMWilliam C Swope - IBMTodd J Martínez - Stanford UniversityVijay S Pande - Stanford University
- Resource Type
- Journal article
- Publication Details
- The journal of physical chemistry. B, Vol.121(16), pp.4023-4039
- DOI
- 10.1021/acs.jpcb.7b02320
- PMID
- 28306259
- ISSN
- 1520-6106
- eISSN
- 1520-5207
- Grant note
- U19 AI109662 / NIAID NIH HHS P30 CA008748 / NCI NIH HHS R01 GM062868 / NIGMS NIH HHS
- Language
- English
- Date published
- 04/27/2017
- Academic Unit
- Chemical and Biochemical Engineering
- Record Identifier
- 9984197256602771
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