| 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 | 1565 | 2004 |
| 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 | 279 | 2004 |
| Sampling of slow diffusive conformational transitions with accelerated molecular dynamics D Hamelberg, CAF de Oliveira, JA McCammon The Journal of chemical physics 127 (15), 2007 | 255 | 2007 |
| 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 | 222 | 2012 |
| 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 | 152 | 2016 |
| 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 | 139 | 2000 |
| A statistical analysis of the precision of reweighting-based simulations T Shen, D Hamelberg The Journal of chemical physics 129 (3), 2008 | 122 | 2008 |
| 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 | 118 | 2008 |
| 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 | 115 | 2005 |
| 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 | 113 | 2004 |
| 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 | 110 | 2004 |
| 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 | 108 | 2005 |
| 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 | 106 | 2011 |
| 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 | 105 | 2001 |
| 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 | 101 | 2008 |
| 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 | 91 | 2009 |
| 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), 2005 | 90 | 2005 |
| 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 | 82 | 2002 |
| 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 | 79 | 2012 |
| 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 | 77 | 2004 |
Prof. J. Andrew McCammonUniversity of California, San DiegoVerified email at ucsd.edu
