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© Research
Publication : Journal of chemical theory and computation

Assessing the Quality of the OPEP Coarse-Grained Force Field

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of chemical theory and computation - 19 May 2011

Barducci A, Bonomi M, Derreumaux P

Link to Pubmed [PMID] – 26596453

J Chem Theory Comput 2011 Jun;7(6):1928-34

A coarse-grained potential that could accurately describe the overall conformational landscape of proteins would be extremely valuable not only for structure prediction but also for studying protein dynamics, large conformational motions, and intrinsically disordered systems. Here, we assessed the quality of the OPEP coarse-grained potential by comparing the reconstructed free-energy surfaces (FESs) of two prototypical β-hairpin and α-helix peptides to all-atom calculations in explicit solvent. We found remarkable agreement between the OPEP FES and those obtained using atomistic models, despite a general overstabilization of α- and β-structures by the coarse-grained potential. The use of advanced sampling techniques based on metadynamics and parallel tempering guaranteed a thorough exploration of the conformational space accessible to the two peptides studied.

https://www.ncbi.nlm.nih.gov/pubmed/26596453