PubRank

Donald Hamelberg

Author PubWeight™ 34.50‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 A statistical analysis of the precision of reweighting-based simulations. J Chem Phys 2008 1.72
2 Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput 2008 1.52
3 A dry ligand-binding cavity in a solvated protein. Proc Natl Acad Sci U S A 2008 1.47
4 DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives. J Am Chem Soc 2004 1.44
5 Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Proc Natl Acad Sci U S A 2011 1.25
6 Clicking 1,2,4,5-tetrazine and cyclooctynes with tunable reaction rates. Chem Commun (Camb) 2011 1.23
7 Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations. J Chem Theory Comput 2008 1.07
8 Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove. J Am Chem Soc 2002 1.06
9 Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study. J Chem Phys 2007 1.06
10 Characterization of a novel DNA minor-groove complex. Biophys J 2004 1.04
11 The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB J 2005 1.00
12 Resolving the complex role of enzyme conformational dynamics in catalytic function. Proc Natl Acad Sci U S A 2012 0.99
13 Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme. RNA 2010 0.98
14 Structural selectivity of aromatic diamidines. J Med Chem 2004 0.98
15 On the application of accelerated molecular dynamics to liquid water simulations. J Phys Chem B 2006 0.96
16 Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics. J Phys Chem B 2009 0.90
17 Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch. RNA 2011 0.86
18 Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch. Nucleic Acids Res 2009 0.86
19 Molecular cycloencapsulation augments solubility and improves therapeutic index of brominated noscapine in prostate cancer cells. Mol Pharm 2012 0.84
20 Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics. J Chem Phys 2010 0.84
21 Insights on the mechanism of amine oxidation catalyzed by D-arginine dehydrogenase through pH and kinetic isotope effects. J Am Chem Soc 2011 0.83
22 The role of conserved water molecules in the catalytic domain of protein kinases. Proteins 2009 0.83
23 Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover. Biophys J 2013 0.83
24 Identification of an L-phenylalanine binding site enhancing the cooperative responses of the calcium-sensing receptor to calcium. J Biol Chem 2014 0.83
25 Accelerated entropy estimates with accelerated dynamics. J Chem Phys 2007 0.81
26 Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers 2007 0.81
27 Mapping the tropomyosin isoform 5 binding site on human erythrocyte tropomodulin: further insights into E-Tmod/TM5 interaction. Arch Biochem Biophys 2005 0.81
28 Elasticity of peptide omega bonds. Phys Rev E Stat Nonlin Soft Matter Phys 2006 0.79
29 Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1. Biochemistry 2014 0.78
30 Extracellular calcium modulates actions of orthosteric and allosteric ligands on metabotropic glutamate receptor 1α. J Biol Chem 2013 0.78
31 Conformational selection in the recognition of phosphorylated substrates by the catalytic domain of human Pin1. Biochemistry 2011 0.78
32 The cluster of hydrophobic residues controls the entrance to the active site of choline oxidase. Biochemistry 2009 0.77
33 Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design. J Chem Inf Model 2013 0.76
34 The dilemma of conformational dynamics in enzyme catalysis: perspectives from theory and experiment. Adv Exp Med Biol 2014 0.76
35 Cyclodextrin complexes of reduced bromonoscapine in guar gum microspheres enhance colonic drug delivery. Mol Pharm 2014 0.75
36 Conformation-directed catalysis and coupled enzyme-substrate dynamics in Pin1 phosphorylation-dependent cis-trans isomerase. J Phys Chem B 2013 0.75
37 Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis-tau peptide. Proteins 2015 0.75
38 Experimental studies of the Universal Chemical Key (UCK) algorithm on the NCI database of chemical compounds. Proc IEEE Comput Soc Bioinform Conf 2003 0.75
39 High-pressure effect on the dynamics of solvated peptides. J Chem Phys 2012 0.75
40 Enzyme Mediated Conversion of FAD to 8-formyl FAD in Formate Oxidase Results in Modified Cofactor with Enhanced Catalytic Properties. Biochemistry 2017 0.75
41 Entropic and surprisingly small intramolecular polarization effects in the mechanism of cyclophilin A. J Phys Chem B 2012 0.75
42 Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective. J Phys Chem B 2017 0.75
43 An empirical study of the universal chemical key algorithm for assigning unique keys to chemical compounds. J Bioinform Comput Biol 2004 0.75