. "14310" . "Zacharias, Martin" . "Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation" . . "Mishra, Sushil Kumar" . "2"^^ . "1" . . "Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation"@en . "Glycobiology" . "15"^^ . . "000330838800008" . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . "Ko\u010Da, Jaroslav" . . "Kara, Mahmut" . . "Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation" . . . . "24" . . "http://glycob.oxfordjournals.org/content/24/1/70" . . "Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides." . . . "Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides."@en . "P(ED1.1.00/02.0068), P(EE2.3.30.0009), P(GA13-25401S)" . "[0A5A8CD77F42]" . "14662" . . . "RIV/00216224:14310/14:00073439" . "adaptive biasing force simulations; biasing potential; replica-exchange simulation; conformational sampling; molecular dynamics simulation; saccharides"@en . "10.1093/glycob/cwt093" . . "Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation"@en . "0959-6658" . . "4"^^ . . . . . "RIV/00216224:14310/14:00073439!RIV15-MSM-14310___" .