Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

Lee-Ping Wang; Keri A McKiernan; Joseph Gomes; Kyle A Beauchamp; Teresa Head-Gordon; Julia E Rice; William C Swope; Todd J Martínez; Vijay S Pande

doi:10.1021/acs.jpcb.7b02320

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Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

Journal article

Open access

Peer reviewed

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

Lee-Ping Wang, Keri A McKiernan, Joseph Gomes, Kyle A Beauchamp, Teresa Head-Gordon, Julia E Rice, William C Swope, Todd J Martínez and Vijay S Pande

The journal of physical chemistry. B, Vol.121(16), pp.4023-4039

04/27/2017

DOI: 10.1021/acs.jpcb.7b02320

PMID: 28306259

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https://www.ncbi.nlm.nih.gov/pmc/articles/9724927View

Open Access

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.

Software

Thermodynamics

Databases, Protein

Molecular Dynamics Simulation

Protein Denaturation

Proteins - chemistry

Quantum Theory

Water - chemistry

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, Davis
Keri A McKiernan - Stanford University
Joseph Gomes - Stanford University
Kyle A Beauchamp - Counsyl
Teresa Head-Gordon - Lawrence Berkeley National Laboratory
Julia E Rice - IBM
William C Swope - IBM
Todd J Martínez - Stanford University
Vijay 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
NLM abbreviation: J Phys Chem B
ISSN: 1520-6106
eISSN: 1520-5207
Publisher: American Chemical Society
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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