{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["107(11)"],"submitter":["Abrams CF"],"pubmed_abstract":["We show how to apply the method of temperature-accelerated molecular dynamics (TAMD) in collective variables [Maragliano L, Vanden-Eijnden E (2006) Chem Phys Lett 426:168-175] to sample the conformational space of multidomain proteins in all-atom, explicitly solvated molecular dynamics simulations. The method allows the system to hyperthermally explore the free-energy surface in a set of collective variables computed at the physical temperature. As collective variables, we pick Cartesian coordinates of centers of contiguous subdomains. The method is applied to the GroEL subunit, a 55-kDa, three-domain protein, and HIV-1 gp120. For GroEL, the method induces in about 40 ns conformational changes that recapitulate the t --> r('') transition and are not observed in unaccelerated molecular dyna"],"journal":["Proceedings of the National Academy of Sciences of the United States of America"],"pagination":["4961-6"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC2841907"],"repository":["biostudies-literature"],"pubmed_title":["Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics."],"pmcid":["PMC2841907"],"pubmed_authors":["Abrams CF","Vanden-Eijnden E"],"additional_accession":[]},"is_claimable":false,"name":"Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.","description":"We show how to apply the method of temperature-accelerated molecular dynamics (TAMD) in collective variables [Maragliano L, Vanden-Eijnden E (2006) Chem Phys Lett 426:168-175] to sample the conformational space of multidomain proteins in all-atom, explicitly solvated molecular dynamics simulations. The method allows the system to hyperthermally explore the free-energy surface in a set of collective variables computed at the physical temperature. As collective variables, we pick Cartesian coordinates of centers of contiguous subdomains. The method is applied to the GroEL subunit, a 55-kDa, three-domain protein, and HIV-1 gp120. For GroEL, the method induces in about 40 ns conformational changes that recapitulate the t --> r('') transition and are not observed in unaccelerated molecular dyna","dates":{"release":"2010-01-01T00:00:00Z","publication":"2010 Mar","modification":"2025-04-22T20:17:12.532Z","creation":"2019-03-27T00:29:33Z"},"accession":"S-EPMC2841907","cross_references":{"pubmed":["20194785"],"doi":["10.1073/pnas.0914540107"]}}