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Title: Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States
Authors: Palazzesi, Ferruccio
Prakash, Meher K.
Bonomi, Massimiliano
Barducci, Alessandro
Keywords: Physical Chemistry
Atomic, Molecular & Chemical Physics
Molecular-Dynamics Simulations
Replica-Averaged Metadynamics
Well-Tempered Metadynamics
Folding Simulations
Structural Dynamics
Dipolar Couplings
Issue Date: 2015
Publisher: American Chemical Society
Citation: Journal of Chemical Theory and Computation
Palazzesi, F.; Prakash, M. K.; Bonomi, M.; Barducci, A., Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States. Journal of Chemical Theory and Computation 2015, 11 (1), 2-7.
Abstract: Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by combining enhanced-sampling MD simulations with NMR data. These force-fields generate significantly different conformational ensembles, and AMBER03w [Best and Mittal J. Phys. Chem. B 2010, 114, 14916-14923] provides the best agreement with experiments, which is further improved by adding the ILDN corrections [Lindorff-Larsen et al. Proteins 2010, 78, 1950-1958].
Description: Restricted access
ISSN: 1549-9618
Appears in Collections:Research Articles (Meher K. Prakash)

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