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PACSAB: Coarse-Grained Force Field for the Study of Protein–Protein Interactions and Conformational Sampling in Multiprotein Systems

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journal contribution
posted on 08.12.2015, 00:00 by Agustí Emperador, Pedro Sfriso, Marcos Ariel Villarreal, Josep Lluis Gelpí, Modesto Orozco
Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein–protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.