Optimization of protein force-field parameters with the Protein Data Bank

Details Optimization of protein force-field parameters with the Protein Data Bank Optimization of protein force-field parameters with the Protein Data Bank

2003-09-04

arxiv.org/abs/cond-mat/0309110v1

Physics

Condensed Matter

Statistical Mechanics

17 pages, (LaTeX), 5 figures

Scientific paper

10.1016/j.cplett.2003.10.107

We propose a novel method to optimize existing force-field parameters for protein systems. The method consists of minimizing the summation of the square of the force acting on each atom in the proteins with the structures from the Protein Data Bank. We performed this optimization to the partial-charge and torsion-energy parameters of the AMBER parm96 force field, using 100 molecules from the Protein Data Bank. We then performed folding simulations of $\alpha$-helical and $\beta$-hairpin peptides. The optimized force-field parameters gave structures more similar to the experimental implications than the original AMBER force field.

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