Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

By Robert B. Best, Gerhard Hummer. Journal of Physical Chemistry B, 2009

811 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Developing a molecular dynamics force field for both folded and disordered protein states (2018, methodology): “The force fields examined were the Amber force fields a99SB*-ILDN (11, 12) with TIP3P (13), a03ws (8), a99SB-ILDN with TIP4P-D (7), and a99SB with TIP4P-Ew (32) and the Head-Gordon LJ (9) and dihedral (33) modifications (we refer to this force field as a99SB-UCB) as well as the CHARMM force fields…”
Alchemical free energy methods for drug discovery: Progress and challenges (2011, methodology): “More recently, Best and Hummer have used converged replica exchange data to compare the behavior of simulated helices to new experimental data in order to improve force field torsion parameters, with compelling initial results indicating its transferability [103].”
Systematic Validation of Protein Force Fields against Experimental Data (2012, methodology): “The helical fraction of the AAQAA-peptide was calculated as the fraction of helical residues [13,15] at each temperature in the simulated tempering simulations and compared to the experimental values [24].”