Donald Hamelberg
Title
Cited by
Cited by
Year
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules
D Hamelberg, J Mongan, JA McCammon
The Journal of chemical physics 120 (24), 11919-11929, 2004
12712004
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method
D Hamelberg, JA McCammon
Journal of the American Chemical Society 126 (24), 7683-7689, 2004
2592004
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
D Hamelberg, CAF de Oliveira, JA McCammon
The Journal of chemical physics 127 (15), 10B614, 2007
2232007
Clicking 1, 2, 4, 5-tetrazine and cyclooctynes with tunable reaction rates
W Chen, D Wang, C Dai, D Hamelberg, B Wang
Chemical communications 48 (12), 1736-1738, 2012
1762012
Flexible structure of DNA: ion dependence of minor-groove structure and dynamics
D Hamelberg, L McFail-Isom, LD Williams, WD Wilson
Journal of the American Chemical Society 122 (43), 10513-10520, 2000
1362000
A dry ligand-binding cavity in a solvated protein
J Qvist, M Davidovic, D Hamelberg, B Halle
Proceedings of the National Academy of Sciences 105 (17), 6296-6301, 2008
1122008
DNA sequence dependent monomer− dimer binding modulation of asymmetric benzimidazole derivatives
FA Tanious, D Hamelberg, C Bailly, A Czarny, DW Boykin, WD Wilson
Journal of the American Chemical Society 126 (1), 143-153, 2004
1102004
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine− proline motifs: accelerated molecular dynamics analysis
D Hamelberg, T Shen, JA McCammon
Journal of the American Chemical Society 127 (6), 1969-1974, 2005
1072005
A statistical analysis of the precision of reweighting-based simulations
T Shen, D Hamelberg
The Journal of chemical physics 129 (3), 034103, 2008
1052008
Fast peptidyl cis− trans isomerization within the flexible gly-rich flaps of HIV-1 protease
D Hamelberg, JA McCammon
Journal of the American Chemical Society 127 (40), 13778-13779, 2005
1042005
Characterization of a novel DNA minor-groove complex
B Nguyen, D Hamelberg, C Bailly, P Colson, J Stanek, R Brun, S Neidle, ...
Biophysical journal 86 (2), 1028-1041, 2004
1032004
Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects
D Hamelberg, LD Williams, WD Wilson
Journal of the American Chemical Society 123 (32), 7745-7755, 2001
1032001
Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation
U Doshi, MJ Holliday, EZ Eisenmesser, D Hamelberg
Proceedings of the National Academy of Sciences 113 (17), 4735-4740, 2016
1012016
Replica-exchange accelerated molecular dynamics (REXAMD) applied to thermodynamic integration
M Fajer, D Hamelberg, JA McCammon
Journal of chemical theory and computation 4 (10), 1565-1569, 2008
912008
Protein conformational dynamics in the mechanism of HIV-1 protease catalysis
VY Torbeev, H Raghuraman, D Hamelberg, M Tonelli, WM Westler, ...
Proceedings of the National Academy of Sciences 108 (52), 20982-20987, 2011
892011
Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations
D Hamelberg, T Shen, J Andrew McCammon
The Journal of chemical physics 122 (24), 241103, 2005
832005
Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove
B Nguyen, MPH Lee, D Hamelberg, A Joubert, C Bailly, R Brun, S Neidle, ...
Journal of the American Chemical Society 124 (46), 13680-13681, 2002
792002
Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics
U Doshi, D Hamelberg
The Journal of Physical Chemistry B 113 (52), 16590-16595, 2009
772009
Resolving the complex role of enzyme conformational dynamics in catalytic function
U Doshi, LC McGowan, ST Ladani, D Hamelberg
Proceedings of the National Academy of Sciences 109 (15), 5699-5704, 2012
732012
Structural selectivity of aromatic diamidines
JB Chaires, J Ren, D Hamelberg, A Kumar, V Pandya, DW Boykin, ...
Journal of medicinal chemistry 47 (23), 5729-5742, 2004
692004
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Articles 1–20