| Year |
Citation |
Score |
| 2023 |
Ahmed F, Yao XQ, Hamelberg D. Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins. The Journal of Physical Chemistry. B. 127: 3139-3150. PMID 36989346 DOI: 10.1021/acs.jpcb.2c08650 |
0.369 |
|
| 2023 |
Ouedraogo D, Souffrant M, Yao XQ, Hamelberg D, Gadda G. Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase. Biochemistry. PMID 36795942 DOI: 10.1021/acs.biochem.2c00697 |
0.395 |
|
| 2022 |
Kumutima J, Yao XQ, Hamelberg D. Post-translational Modifications of Cyclophilin D Fine-Tune Its Conformational Dynamics and Activity: Implications for Its Mitochondrial Function. The Journal of Physical Chemistry. B. 126: 10844-10853. PMID 36529932 DOI: 10.1021/acs.jpcb.2c06208 |
0.378 |
|
| 2022 |
Yao XQ, Hamelberg D. Residue-Residue Contact Changes during Functional Processes Define Allosteric Communication Pathways. Journal of Chemical Theory and Computation. 18: 1173-1187. PMID 35048691 DOI: 10.1021/acs.jctc.1c00669 |
0.307 |
|
| 2021 |
Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G. A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry. PMID 33630571 DOI: 10.1021/acs.biochem.1c00054 |
0.422 |
|
| 2020 |
Deng X, Xin Y, Miller CL, Hamelberg D, Kirberger M, Moremen KW, Hu J, Yang JJ. Structural Mechanism of Cooperative Regulation of Calcium-Sensing Receptor-Mediated Cellular Signaling. Current Opinion in Physiology. 17: 269-277. PMID 33709045 DOI: 10.1016/J.Cophys.2020.08.020 |
0.314 |
|
| 2020 |
Ahmed F, Yao X, Hamelberg D. Key Dynamic Residues in the Catalytic Activity of Human Cyclophilins Identified with a Dynamical Evolution Analysis The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.00249 |
0.407 |
|
| 2020 |
Souffrant MG, Yao X, Momin M, Hamelberg D. N-Glycosylation and Gaucher Disease Mutation Allosterically Alter Active-Site Dynamics of Acid-β-Glucosidase Acs Catalysis. 10: 1810-1820. DOI: 10.1021/Acscatal.9B04404 |
0.408 |
|
| 2020 |
Ho KC, Hamelberg D. Automatic Partition of Protein Molecular Dynamics using Coupled Hidden Markov-Ising Models Biophysical Journal. 118: 143a. DOI: 10.1016/J.Bpj.2019.11.904 |
0.356 |
|
| 2019 |
Yao XQ, Hamelberg D. Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis. Accounts of Chemical Research. PMID 31793290 DOI: 10.1016/J.Bpj.2019.11.1716 |
0.473 |
|
| 2019 |
Childers KC, Yao XQ, Giannakoulias S, Amason J, Hamelberg D, Garcin ED. Synergistic mutations in soluble guanylyl cyclase (sGC) reveal a key role for interfacial regions in the sGC activation mechanism. The Journal of Biological Chemistry. PMID 31645439 DOI: 10.1074/Jbc.Ra119.011010 |
0.365 |
|
| 2019 |
Owens EA, Huynh HT, Stroeva E, Barman A, Ziabrev K, Paul A, Nguyen SV, Laramie MD, Hamelberg D, Germann MW, Wilson WD, Henary M. Second Generation G-Quadruplex Stabilizing Trimethine Cyanines. Bioconjugate Chemistry. PMID 31518105 DOI: 10.1021/Acs.Bioconjchem.9B00571 |
0.31 |
|
| 2019 |
Yao XQ, Momin M, Hamelberg D. Establishing a Framework of Using Residue-Residue Interactions in Protein Difference Network Analysis. Journal of Chemical Information and Modeling. PMID 31268315 DOI: 10.1021/Acs.Jcim.9B00320 |
0.336 |
|
| 2019 |
Chun Ho K, Hamelberg D. Dynamic Combinatorial Analysis of Local Configurations in Molecular Dynamics Simulation: Frequent Itemset Mining and Hierarchical Hidden Markov Model Biophysical Journal. 116: 166a. DOI: 10.1016/J.Bpj.2018.11.923 |
0.377 |
|
| 2018 |
Ho KC, Hamelberg D. Combinatorial Coarse-Graining of Molecular Dynamics Simulations for Detecting Relationships between Local Configurations and Overall Conformations. Journal of Chemical Theory and Computation. PMID 30351007 DOI: 10.1021/Acs.Jctc.8B00333 |
0.35 |
|
| 2018 |
Yao XQ, Momin MF, Hamelberg D. Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis. Journal of Chemical Information and Modeling. PMID 29956925 DOI: 10.1021/Acs.Jcim.8B00250 |
0.34 |
|
| 2018 |
Rodriguez-Bussey I, Yao XQ, Shouaib AD, Lopez J, Hamelberg D. Decoding Allosteric Communication Pathways in Cyclophilin A with a Comparative Analysis of Perturbed Conformational Ensembles. The Journal of Physical Chemistry. B. PMID 29852734 DOI: 10.1021/Acs.Jpcb.8B03824 |
0.469 |
|
| 2018 |
Momin MF, Yao XQ, Thor W, Hamelberg D. Substrate Sequence Determines Catalytic Activities, Domain-Binding Preferences, and Allosteric Mechanisms in Pin1. The Journal of Physical Chemistry. B. PMID 29851476 DOI: 10.1021/Acs.Jpcb.8B03819 |
0.377 |
|
| 2018 |
Vu PJ, Yao X, Momin M, Hamelberg D. Unraveling Allosteric Mechanisms of Enzymatic Catalysis with an Evolutionary Analysis of Residue–Residue Contact Dynamical Changes Acs Catalysis. 8: 2375-2384. DOI: 10.1021/Acscatal.7B04263 |
0.503 |
|
| 2018 |
Vu PJ, Yao X, Momin M, Hamelberg D. Evolutionarily Conserved and Divergent Residue-Residue Contact Dynamics Provide Insights into the Allosteric Regulation of Cyclophilins Biophysical Journal. 114: 337a. DOI: 10.1016/J.Bpj.2017.11.1885 |
0.429 |
|
| 2017 |
Robbins JM, Souffrant MG, Hamelberg D, Gadda G, Bommarius AS. Enzyme Mediated Conversion of FAD to 8-formyl FAD in Formate Oxidase Results in Modified Cofactor with Enhanced Catalytic Properties. Biochemistry. PMID 28640638 DOI: 10.1021/Acs.Biochem.7B00335 |
0.466 |
|
| 2017 |
Momin MF, Xin Y, Hamelberg D. Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective. The Journal of Physical Chemistry. B. PMID 28570811 DOI: 10.1021/Acs.Jpcb.7B03470 |
0.47 |
|
| 2017 |
Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa D-Arginine Dehydrogenase. Biochemistry. PMID 28445031 DOI: 10.1021/Acs.Biochem.7B00098 |
0.481 |
|
| 2017 |
Hamelberg D. Coupled Residue-Residue Dynamics in Protein Allosteric Mechanisms Biophysical Journal. 112: 465a. DOI: 10.1016/J.Bpj.2016.11.2490 |
0.51 |
|
| 2016 |
Barman A, Hamelberg D. Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1. The Journal of Physical Chemistry. B. PMID 27077947 DOI: 10.1021/Acs.Jpcb.6B02123 |
0.404 |
|
| 2016 |
Doshi U, Holliday MJ, Eisenmesser EZ, Hamelberg D. Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation. Proceedings of the National Academy of Sciences of the United States of America. 113: 4735-40. PMID 27071107 DOI: 10.1073/Pnas.1523573113 |
0.479 |
|
| 2016 |
Salvi F, Rodriguez I, Hamelberg D, Gadda G. Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase. Biochemistry. 55: 1473-84. PMID 26907558 DOI: 10.1021/Acs.Biochem.5B01356 |
0.359 |
|
| 2016 |
Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. Journal of Chemical Information and Modeling. 56: 139-47. PMID 26651388 DOI: 10.1021/Acs.Jcim.5B00560 |
0.411 |
|
| 2016 |
Rodriguez-Bussey IG, Doshi U, Hamelberg D. Enhanced molecular dynamics sampling of drug target conformations. Biopolymers. 105: 35-42. PMID 26352326 DOI: 10.1002/Bip.22740 |
0.383 |
|
| 2016 |
Romero E, Ladani ST, Hamelberg D, Gadda G. Solvent-Slaved Motions in the Hydride Tunneling Reaction Catalyzed by Human Glycolate Oxidase Acs Catalysis. 6: 2113-2120. DOI: 10.1021/Acscatal.5B02889 |
0.439 |
|
| 2015 |
Ho KC, Hamelberg D. Oscillatory Diffusion and Second Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation. Journal of Chemical Theory and Computation. PMID 26636883 DOI: 10.1021/Acs.Jctc.5B00876 |
0.341 |
|
| 2015 |
Barman A, Batiste B, Hamelberg D. Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins. Journal of Chemical Theory and Computation. 11: 1854-63. PMID 26574391 DOI: 10.1021/Ct501036R |
0.466 |
|
| 2015 |
Liu F, Geng J, Gumpper RH, Barman A, Davis I, Ozarowski A, Hamelberg D, Liu A. An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. The Journal of Biological Chemistry. 290: 15621-34. PMID 25918158 DOI: 10.1074/Jbc.M115.650259 |
0.312 |
|
| 2015 |
Mishra RC, Gundala SR, Karna P, Lopus M, Gupta KK, Nagaraju M, Hamelberg D, Tandon V, Panda D, Reid MD, Aneja R. Design, synthesis and biological evaluation of di-substituted noscapine analogs as potent and microtubule-targeted anticancer agents. Bioorganic & Medicinal Chemistry Letters. 25: 2133-40. PMID 25891106 DOI: 10.1016/J.Bmcl.2015.03.076 |
0.322 |
|
| 2015 |
Velazquez HA, Hamelberg D. Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations. The Journal of Chemical Physics. 142: 075102. PMID 25702031 DOI: 10.1063/1.4907884 |
0.701 |
|
| 2015 |
Ladani ST, Souffrant MG, Barman A, Hamelberg D. Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases. Biochimica Et Biophysica Acta. 1850: 1994-2004. PMID 25585011 DOI: 10.1016/J.Bbagen.2014.12.023 |
0.379 |
|
| 2015 |
Barman A, Hamelberg D. Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis-tau peptide. Proteins. 83: 436-44. PMID 25524218 DOI: 10.1002/Prot.24740 |
0.391 |
|
| 2015 |
Doshi U, Hamelberg D. Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics. Biochimica Et Biophysica Acta. 1850: 878-88. PMID 25153688 DOI: 10.1016/J.Bbagen.2014.08.003 |
0.402 |
|
| 2014 |
Doshi U, Hamelberg D. Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent. The Journal of Physical Chemistry Letters. 5: 1217-24. PMID 26274474 DOI: 10.1021/Jz500179A |
0.446 |
|
| 2014 |
Barman A, Hamelberg D. Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1. Biochemistry. 53: 3839-50. PMID 24840168 DOI: 10.1021/Bi5000977 |
0.528 |
|
| 2014 |
Doshi U, Hamelberg D. The dilemma of conformational dynamics in enzyme catalysis: perspectives from theory and experiment. Advances in Experimental Medicine and Biology. 805: 221-43. PMID 24446364 DOI: 10.1007/978-3-319-02970-2_10 |
0.519 |
|
| 2014 |
Tork Ladani S, Hamelberg D. Intricacies of interactions, dynamics and solvent effects in enzyme catalysis: A computational perspective on cyclophilin A Molecular Simulation. 40: 765-776. DOI: 10.1080/08927022.2014.919498 |
0.595 |
|
| 2013 |
Velazquez HA, Hamelberg D. Conformation-directed catalysis and coupled enzyme-substrate dynamics in Pin1 phosphorylation-dependent cis-trans isomerase. The Journal of Physical Chemistry. B. 117: 11509-17. PMID 23980573 DOI: 10.1021/Jp405271S |
0.745 |
|
| 2013 |
McGowan LC, Hamelberg D. Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover. Biophysical Journal. 104: 216-26. PMID 23332074 DOI: 10.1016/J.Bpj.2012.11.3815 |
0.573 |
|
| 2013 |
Nagaraju M, McGowan LC, Hamelberg D. Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design. Journal of Chemical Information and Modeling. 53: 403-10. PMID 23312027 DOI: 10.1021/Ci300432W |
0.565 |
|
| 2013 |
Zhang C, Zhuo Y, Feng J, Strachan H, Mulpuri N, Hamelberg D, Moremen K, Brown EM, Yang JJ. Hetero Interaction with an Amino Acid Globally Enhances Cooperative Activation of CaSR in Response to Extracellular Signaling Biophysical Journal. 104: 402a-403a. DOI: 10.1016/J.Bpj.2012.11.2246 |
0.309 |
|
| 2012 |
Doshi U, Hamelberg D. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. Journal of Chemical Theory and Computation. 8: 4004-12. PMID 26605567 DOI: 10.1021/Ct3004194 |
0.346 |
|
| 2012 |
Ladani ST, Hamelberg D. Entropic and surprisingly small intramolecular polarization effects in the mechanism of cyclophilin A. The Journal of Physical Chemistry. B. 116: 10771-8. PMID 22891696 DOI: 10.1021/Jp305917C |
0.535 |
|
| 2012 |
Nellas RB, Glover MM, Hamelberg D, Shen T. High-pressure effect on the dynamics of solvated peptides. The Journal of Chemical Physics. 136: 145103. PMID 22502549 DOI: 10.1063/1.3700183 |
0.358 |
|
| 2012 |
Doshi U, McGowan LC, Ladani ST, Hamelberg D. Resolving the complex role of enzyme conformational dynamics in catalytic function. Proceedings of the National Academy of Sciences of the United States of America. 109: 5699-704. PMID 22451902 DOI: 10.1073/Pnas.1117060109 |
0.513 |
|
| 2012 |
Doshi U, Kelley JM, Hamelberg D. Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch Rna. 18: 300-307. PMID 22194311 DOI: 10.1261/Rna.028779.111 |
0.331 |
|
| 2011 |
Doshi U, Hamelberg D. Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers' Theory. Journal of Chemical Theory and Computation. 7: 575-81. PMID 26596291 DOI: 10.1021/Ct1005399 |
0.443 |
|
| 2011 |
Torbeev VY, Raghuraman H, Hamelberg D, Tonelli M, Westler WM, Perozo E, Kent SB. Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Proceedings of the National Academy of Sciences of the United States of America. 108: 20982-7. PMID 22158985 DOI: 10.1073/Pnas.1111202108 |
0.438 |
|
| 2011 |
Yuan H, Xin Y, Hamelberg D, Gadda G. Insights on the mechanism of amine oxidation catalyzed by D-arginine dehydrogenase through pH and kinetic isotope effects. Journal of the American Chemical Society. 133: 18957-65. PMID 21999550 DOI: 10.1021/Ja2082729 |
0.412 |
|
| 2011 |
Velazquez HA, Hamelberg D. Conformational selection in the recognition of phosphorylated substrates by the catalytic domain of human Pin1. Biochemistry. 50: 9605-15. PMID 21967280 DOI: 10.1021/Bi2009954 |
0.729 |
|
| 2011 |
Velazquez HA, Hamelberg D. Ionic, Hydrogen Bond, and π-Cation Interactions Chemosensors: Principles, Strategies, and Applications. 19-24. DOI: 10.1002/9781118019580.ch2 |
0.583 |
|
| 2010 |
Johnson Q, Doshi U, Shen T, Hamelberg D. Water's Contribution to the Energetic Roughness from Peptide Dynamics. Journal of Chemical Theory and Computation. 6: 2591-7. PMID 26616063 DOI: 10.1021/Ct100183S |
0.423 |
|
| 2010 |
Xin Y, Hamelberg D. Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme. Rna (New York, N.Y.). 16: 2455-63. PMID 20971809 DOI: 10.1261/Rna.2334110 |
0.35 |
|
| 2010 |
Xin Y, Doshi U, Hamelberg D. Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics. The Journal of Chemical Physics. 132: 224101. PMID 20550384 DOI: 10.1063/1.3432761 |
0.424 |
|
| 2010 |
Kelley JM, Hamelberg D. Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch. Nucleic Acids Research. 38: 1392-400. PMID 19969538 DOI: 10.1093/Nar/Gkp1106 |
0.385 |
|
| 2009 |
Doshi U, Hamelberg D. Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics. The Journal of Physical Chemistry. B. 113: 16590-5. PMID 19938868 DOI: 10.1021/Jp907388M |
0.405 |
|
| 2009 |
Xin Y, Gadda G, Hamelberg D. The cluster of hydrophobic residues controls the entrance to the active site of choline oxidase. Biochemistry. 48: 9599-605. PMID 19728743 DOI: 10.1021/Bi901295A |
0.475 |
|
| 2009 |
Knight JD, Hamelberg D, McCammon JA, Kothary R. The role of conserved water molecules in the catalytic domain of protein kinases. Proteins. 76: 527-35. PMID 19425109 DOI: 10.1002/Prot.22451 |
0.334 |
|
| 2009 |
Hamelberg D, McCammon JA. Mechanistic insight into the role of transition-state stabilization in cyclophilin A. Journal of the American Chemical Society. 131: 147-52. PMID 19128175 DOI: 10.1021/Ja806146G |
0.522 |
|
| 2008 |
Fajer M, Hamelberg D, McCammon JA. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. Journal of Chemical Theory and Computation. 4: 1565-1569. PMID 19461870 DOI: 10.1021/Ct800250M |
0.367 |
|
| 2008 |
de Oliveira CA, Hamelberg D, McCammon JA. Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations. Journal of Chemical Theory and Computation. 4: 1516-1525. PMID 19461868 DOI: 10.1021/Ct800160Q |
0.349 |
|
| 2008 |
Shen T, Hamelberg D. A statistical analysis of the precision of reweighting-based simulations. The Journal of Chemical Physics. 129: 034103. PMID 18647012 DOI: 10.1063/1.2944250 |
0.329 |
|
| 2008 |
Qvist J, Davidovic M, Hamelberg D, Halle B. A dry ligand-binding cavity in a solvated protein. Proceedings of the National Academy of Sciences of the United States of America. 105: 6296-301. PMID 18427121 DOI: 10.1073/Pnas.0709844105 |
0.331 |
|
| 2007 |
de Oliveira CA, Hamelberg D, McCammon JA. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study. The Journal of Chemical Physics. 127: 175105. PMID 17994855 DOI: 10.1063/1.2794763 |
0.418 |
|
| 2007 |
Hamelberg D, de Oliveira CA, McCammon JA. Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. The Journal of Chemical Physics. 127: 155102. PMID 17949218 DOI: 10.1063/1.2789432 |
0.371 |
|
| 2007 |
Minh DD, Hamelberg D, McCammon JA. Accelerated entropy estimates with accelerated dynamics. The Journal of Chemical Physics. 127: 154105. PMID 17949130 DOI: 10.1063/1.2794754 |
0.357 |
|
| 2007 |
Hamelberg D, Shen T, McCammon JA. A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw. Proceedings of the National Academy of Sciences of the United States of America. 104: 14947-51. PMID 17823247 DOI: 10.1073/Pnas.0703151104 |
0.365 |
|
| 2007 |
Sørensen J, Hamelberg D, Schiøtt B, McCammon JA. Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers. 86: 73-82. PMID 17315201 DOI: 10.1002/Bip.20705 |
0.331 |
|
| 2006 |
de Oliveira CA, Hamelberg D, McCammon JA. On the application of accelerated molecular dynamics to liquid water simulations. The Journal of Physical Chemistry. B. 110: 22695-701. PMID 17092018 DOI: 10.1021/Jp062845O |
0.366 |
|
| 2006 |
Hamelberg D, Shen T, McCammon JA. Insight into the role of hydration on protein dynamics. The Journal of Chemical Physics. 125: 094905. PMID 16965117 DOI: 10.1063/1.2232131 |
0.377 |
|
| 2006 |
Shen T, Hamelberg D, McCammon JA. Elasticity of peptide omega bonds. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 73: 041908. PMID 16711837 DOI: 10.1103/Physreve.73.041908 |
0.413 |
|
| 2006 |
Hamelberg D, McCammon JA. Chapter 12 Accelerating Conformational Transitions in Biomolecular Simulations Annual Reports in Computational Chemistry. 2: 221-232. DOI: 10.1016/S1574-1400(06)02012-3 |
0.397 |
|
| 2005 |
Vera C, Lao J, Hamelberg D, Sung LA. Mapping the tropomyosin isoform 5 binding site on human erythrocyte tropomodulin: further insights into E-Tmod/TM5 interaction. Archives of Biochemistry and Biophysics. 444: 130-8. PMID 16297372 DOI: 10.1016/J.Abb.2005.10.002 |
0.301 |
|
| 2005 |
Hamelberg D, McCammon JA. Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. Journal of the American Chemical Society. 127: 13778-9. PMID 16201784 DOI: 10.1021/Ja054338A |
0.358 |
|
| 2005 |
Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 19: 1389-95. PMID 16126906 DOI: 10.1096/Fj.04-3590Hyp |
0.382 |
|
| 2005 |
Hamelberg D, Shen T, Andrew McCammon J. Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations. The Journal of Chemical Physics. 122: 241103. PMID 16035738 DOI: 10.1063/1.1942487 |
0.422 |
|
| 2005 |
Hamelberg D, Shen T, McCammon JA. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. Journal of the American Chemical Society. 127: 1969-74. PMID 15701032 DOI: 10.1021/Ja0446707 |
0.478 |
|
| 2004 |
Hamelberg D, Mongan J, McCammon JA. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. The Journal of Chemical Physics. 120: 11919-29. PMID 15268227 DOI: 10.1063/1.1755656 |
0.379 |
|
| 2004 |
Hamelberg D, McCammon JA. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. Journal of the American Chemical Society. 126: 7683-9. PMID 15198616 DOI: 10.1021/Ja0377908 |
0.348 |
|
| 2004 |
Nguyen B, Hamelberg D, Bailly C, Colson P, Stanek J, Brun R, Neidle S, Wilson WD. Characterization of a Novel DNA Minor-Groove Complex Biophysical Journal. 86: 1028-1041. PMID 14747338 DOI: 10.1016/S0006-3495(04)74178-8 |
0.322 |
|
| 2004 |
Tanious FA, Hamelberg D, Bailly C, Czarny A, Boykin DW, Wilson WD. DNA Sequence Dependent Monomer-Dimer Binding Modulation of Asymmetric Benzimidazole Derivatives Journal of the American Chemical Society. 126: 143-153. PMID 14709078 DOI: 10.1021/Ja030403+ |
0.333 |
|
| 2002 |
Nguyen B, Lee MPH, Hamelberg D, Joubert A, Bailly C, Brun R, Neidle S, Wilson WD. Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove Journal of the American Chemical Society. 124: 13680-13681. PMID 12431090 DOI: 10.1021/Ja027953C |
0.323 |
|
| 2002 |
Hamelberg D, Williams LD, Wilson WD. Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies. Nucleic Acids Research. 30: 3615-23. PMID 12177304 DOI: 10.1093/Nar/Gkf472 |
0.351 |
|
| 2000 |
Hamelberg D, McFail-Isom L, Williams LD, David Wilson W. Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics Journal of the American Chemical Society. 122: 10513-10520. DOI: 10.1021/Ja000707L |
0.306 |
|
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