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© Research
Publication : Journal of chemical theory and computation

Accuracy of current all-atom force-fields in modeling protein disordered states

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of chemical theory and computation - 01 Jan 2015

Palazzesi F, Prakash MK, Bonomi M, Barducci A

Link to Pubmed [PMID] – 26574197

J. Chem. Theory Comput. 11 (2015) 2

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 ].

https://www.ncbi.nlm.nih.gov/pubmed/26574197