Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters

K. J. Bowers, Federico D. Sacerdoti, John K. Salmon, +10

Cluster ComputingEngineeringComputer ArchitectureComputational ChemistryChemistry +19

Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters

K. J. Bowers, David E. Chow, Huafeng Xu, +10

Cluster ComputingEngineeringComputer ArchitectureComputational ChemistryMolecular Dynamics +17

Pathway and mechanism of drug binding to G-protein-coupled receptors

Ron O. Dror, Albert C. Pan, Daniel H. Arlow, +5

Proceedings of the National Academy of Sciences

Drug TargetPeptide ScienceDrug EntryMolecular DynamicsMolecular Pharmacology +19

Activation mechanism of the<i>β</i>₂-adrenergic receptor

Ron O. Dror, Daniel H. Arlow, Paul Maragakis, +5

Proceedings of the National Academy of Sciences

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

Tai‐Sung Lee, Bryce K. Allen, Timothy J. Giese, +11

Journal of Chemical Information and Modeling

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody

Aaron G. Schmidt, Huafeng Xu, Amir R. Khan, +15

Proceedings of the National Academy of Sciences

VaccinationInfluenza HaImmunologyMolecular BiologyVirology +10

A conserved protonation-dependent switch controls drug binding in the Abl kinase

Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, +6

Proceedings of the National Academy of Sciences

Imatinib BindingProtein AssemblyMolecular BiologyCellular PharmacologyMolecular Dynamics +23

Hydrogen-Bond Kinetics in the Solvation Shell of a Polypeptide

Huafeng Xu, B. J. Berne

The Journal of Physical Chemistry B

EngineeringConfined Water HydrodynamicsHydrogen BondsHydrogen BondHydrogen-bonded Liquid +9

Can Water Polarizability Be Ignored in Hydrogen Bond Kinetics?

Huafeng Xu, Harry A. Stern, B. J. Berne

The Journal of Physical Chemistry B

EngineeringComputational ChemistryChemistryMolecular DynamicsSolution (Chemistry) +15

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins

Paul Maragakis, Kresten Lindorff‐Larsen, Michael P. Eastwood, +9

The Journal of Physical Chemistry B