title: PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.
abstract: 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.
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona) , Baldiri i Reixac 10, Barcelona 08028, Spain.|Joint BSC-IRB Research Program in Computational Biology , IRB Barcelona, Barcelona 08028, Spain.
authors.forename: Agustí
authors.initials: A
authors.lastname: Emperador
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona) , Baldiri i Reixac 10, Barcelona 08028, Spain.|Joint BSC-IRB Research Program in Computational Biology , IRB Barcelona, Barcelona 08028, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Sfriso
authors.affiliation: Instituto de Investigaciones en Fisicoquímica de Córdoba - Departamento de Matemática y Física, CONICET-Universidad Nacional de Córdoba , University City, Córdoba 5000, Argentina.
authors.forename: Marcos Ariel
authors.initials: MA
authors.lastname: Villarreal
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona) , Baldiri i Reixac 10, Barcelona 08028, Spain.|Joint BSC-IRB Research Program in Computational Biology , IRB Barcelona, Barcelona 08028, Spain.|Barcelona Supercomputing Center , Jordi Girona 29, Barcelona 08034, Spain.|Departament de Bioquímica, Facultat de Biologia , Avgda Diagonal 645, Barcelona 08028, Spain.
authors.forename: Josep Lluis
authors.initials: JL
authors.lastname: Gelpí
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona) , Baldiri i Reixac 10, Barcelona 08028, Spain.|Joint BSC-IRB Research Program in Computational Biology , IRB Barcelona, Barcelona 08028, Spain.|Barcelona Supercomputing Center , Jordi Girona 29, Barcelona 08034, Spain.|Departament de Bioquímica, Facultat de Biologia , Avgda Diagonal 645, Barcelona 08028, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry*
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D011506:Proteins; C078592:amyloid beta-protein (1-40)