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Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.

Alberto Perez, Justin L MacCallum¹, Emiliano Brini

¹Department of Chemistry, University of Calgary , Calgary, AB T2N 1N4, Canada.

Journal of Chemical Theory and Computation

|November 18, 2015

Summary

We developed Ff12SB-cMAP, a correction to Amber's ff12SB force field and GBneck2 implicit solvent model. This improves biomolecular simulations by enhancing secondary structure prediction accuracy, aligning computational models with experimental data.

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Area of Science:

Biomolecular modeling
Computational chemistry
Protein dynamics

Background:

Force fields like Amber's ff12SB model biomolecular forces accurately.
Implicit solvent models offer computational efficiency but reduce accuracy.
Accurate models are crucial for studying protein conformational preferences and dynamics.

Purpose of the Study:

To develop an improved implicit solvent model for biomolecular simulations.
To enhance the accuracy of the ff12SB force field combined with GBneck2.
To better predict protein secondary structure biases using computational methods.

Main Methods:

Developed an empirical grid-like correction term (Ff12SB-cMAP).
Parametrized Ff12SB-cMAP using experimental protein helicity data.
Validated the model on various peptides and proteins within the Amber package.

Main Results:

Ff12SB-cMAP significantly improves secondary structure prediction accuracy.
The correction enhances the agreement between simulations and experimental observations.
The model successfully addresses limitations of the ff12SB + GBneck2 combination.

Conclusions:

Ff12SB-cMAP offers a more accurate approach for biomolecular simulations using implicit solvent.
This method improves the reliability of computational studies on protein conformational dynamics.
The Ff12SB-cMAP model is available for use in the Amber simulation package.