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Journal of Chemical Theory and Computation|April 26, 2018
CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and FuranosesAsaminew H Aytenfisu, Mingjun Yang, Alexander D MacKerellCarbohydrate Research|March 1, 2019
Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine designAsaminew H Aytenfisu, Raphael Simon, Alexander D MacKerellCarbohydrate Research|February 10, 2018
Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force fieldMingjun Yang, Asaminew H Aytenfisu, Alexander D MacKerellThe Journal of Physical Chemistry. B|August 25, 2022
Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and GlycoproteinsAbhishek A Kognole, Asaminew H Aytenfisu, Alexander D MacKerellJournal of Molecular Modeling|May 25, 2020
Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxidesAbhishek A Kognole, Asaminew H Aytenfisu, Alexander D MacKerellJournal of Chemical Theory and Computation|August 15, 2019
Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate DerivativesPoonam Pandey, Asaminew H Aytenfisu, Alexander D MacKerell, et al.RNA (New York, N.Y.)|September 16, 2015
Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamicsAsaminew H Aytenfisu, Joseph A Liberman, Joseph E Wedekind, et al.Physical Chemistry Chemical Physics : PCCP|January 6, 2023
Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fieldsAlessandro Ruda, Asaminew H Aytenfisu, Thibault Angles d'Ortoli, et al.Journal of Chemical Theory and Computation|January 4, 2017
Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular DynamicsAsaminew H Aytenfisu, Aleksandar Spasic, Alan Grossfield, et al.Journal of Chemical Theory and Computation|May 8, 2014
Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNAAsaminew H Aytenfisu, Aleksandar Spasic, Matthew G Seetin, et al.Pageof 2