Publications

At Department of Chemistry
Georgia State University

  1. Velazquez H. A., Hamelberg D., (2013). Conformation-Directed Catalysis and Coupled Enzyme–Substrate Dynamics in Pin1 Phosphorylation-Dependent Cis–Trans Isomerase Journal of Physical Chemistry B, 117, 11509–11517

  2. Nagaraju M., McGowan L. C., Hamelberg D., (2013). Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design. Journal of Chemical Information and Modeling, 53, 403–410

  3. McGowan L. C., Hamelberg D., (2013). Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover Biophysical Journal, 104, 216-226

  4. Doshi U., Hamelberg D., (2012). Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. Journal of Chemical Theory and Computation, 8, 4004–4012

  5. Tork-Ladani S., Hamelberg D., (2012). Entropic and Surprisingly Small Intramolecular Polarization Effects in the Mechanism of Cyclophilin A. Journal of Physical Chemistry B, 116, 10771–10778

  6. Doshi U., McGowan L. C., Tork-Ladani S., Hamelberg D., (2012). 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, 5699-5704

  7. Madan J., Baruah B., Nagaraju M., Abdalla M. O., Yates C., Turner T., Rangari V., Hamelberg D., Aneja R., (2012). Molecular Cycloencapsulation Augments Solubility and Improves Therapeutic Index of Brominated Noscapine in Prostate Cancer Cells Molecular Pharmaceutics, 9, 1470-1480

  8. Nellas R. B., Glover M. M., Hamelberg D., Shen T., (2012). High-pressure effect on the dynamics of solvated peptides Journal of Chemical Physics, 136, 145103

  9. Doshi U., Kelley J. M., Hamelberg D., (2012). Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch RNA, 18, 300-307

  10. Chen W., Wang D., Dai C., Hamelberg D., Wang B., (2012). Clicking 1,2,4,5-tetrazine and cyclooctynes with tunable reaction rates Chemical Communications , 48, 1736-1738

  11. Torbeeva V. Y., Raghuraman H., Hamelberg D., Tonellie M., Westlere W. M., Perozoa E., Kent S. B. H., (2011). 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, 20982-20987

  12. Yuan H., Xin Y., Hamelberg D., Gadda G., (2011). 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, 18957–18965

  13. Velazquez H. A., Hamelberg D., (2011). Conformational Selection in the Recognition of Phosphorylated Substrates by the Catalytic Domain of Human Pin1 Biochemistry, 50, 9605–9615

  14. Doshi U., Hamelberg D., (2011). Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers’ Theory Journal of Chemical Theory and Computation, 7, 575–581

  15. Velazquez H. A., Hamelberg D., (2011). Ionic, Hydrogen Bond, and π–Cation Interactions in Chemosensors: Principles, Strategies, and Applications (eds B. Wang and E. V. Anslyn), John Wiley & Sons, Inc., Hoboken, NJ, USA

  16. Xin Y., Hamelberg D., (2010). Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme RNA, 16, 2455-2463

  17. Johnson Q., Doshi U., Shen T., Hamelberg D., (2010). Water’s Contribution to the Energetic Roughness from Peptide Dynamics Journal of Chemical Theory and Computation, 6, 2591–2597

  18. Xin Y., Doshi U., Hamelberg D., (2010). Examining the limits of time reweighting and Kramers’ rate theory to obtain correct kinetics from accelerated molecular dynamics Journal of Chemical Physics, 132, 224101

  19. Kelley J. M., Hamelberg D., (2010). Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch Nucleic Acids Research, 38, 1392-1400

  20. Doshi U., Hamelberg D., (2009). Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics Journal of Physical Chemistry B, 113, 16590-16595

  21. Xin Y., Gadda G., Hamelberg D., (2009). Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline Oxidase Biochemistry, 48, 9599-9605

  22. Knight J. D. R., Hamelberg D., McCammon J. A., Kothary R., (2009). The role conserved water molecules in the catalytic domain of protein kinases Proteins: Structure, Function, and Bioinformatics, 76, 527-535

  23. Hamelberg D., McCammon J. A., (2009). Mechanistic Insight into the Role of Transition-State Stabilization in Cyclophilin A. Journal of the American Chemical Society, 131, 147-152

  24. Shen T., Hamelberg D., (2008). A statistical analysis of the precision of reweighting-based simulations Journal of Chemical Physics, 129, 034103

  25. Fajer M., Hamelberg D., McCammon J. A., (2008). Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. Journal of Chemical Theory and Computation, 4, 1565-1569

  26. de Oliveira C. A. F., Hamelberg D., McCammon J. A., (2008). Coupling accelerated molecular dynamics methods with thermodynamic integration simulations. Journal of Chemical Theory and Computation, 4, 1516-1525

  27. Qvist J., Davidovic M., Hamelberg D., Halle B., (2008). A dry ligand-binding cavity in a solvated protein. Proceedings of the National Academy of Sciences of the United States of America, 105, 6296-6301(Cover Issue)

  28. Hamelberg D., Shen T., McCammon J. A., (2007). 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, 14947-14951

  29. Minh D., Hamelberg D., McCammon J. A., (2007). Accelerated entropy estimates with accelerated dynamics. Journal of Chemical Physics, 127, 154105

  30. Hamelberg D., de Oliveira C. A. F., McCammon J. A., (2007). Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. Journal of Chemical Physics, 127, 155102

  31. de Oliveira C. A. F., Hamelberg D., McCammon J. A., (2007). Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine Dipeptide in explicit solvent as a case study. Journal of Chemical Physics, 127, 175105

  32. Hamelberg D., McCammon J. A., (2007). Dealing with bound waters in a site: Do they leave or stay? In "Computational and Structural Approaches to Drug Discovery," R.M. Stroud, Ed., Royal Society of Chemistry, Ch. 5, pp. 95-110

  33. Sørensen J., Hamelberg D., Schiøtt B., McCammon, J. A. (2007). Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers, 86, 73-82 (Cover Issue)

  34. Hamelberg D., McCammon J. A., (2006). Accelerating conformational transitions in biomolecular systems. Annual Reports in Computational Chemistry, 2, 221-232

  35. de Oliveira C. A. F., Hamelberg D., McCammon J. A., (2006). On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations. Journal of Physical Chemistry B, 110, 22695-22701

  36. Hamelberg D., Shen T., McCammon J. A., (2006). Insight into the role of hydration on protein dynamics. Journal Chemical Physics, 125, 094905

  37. Shen T., Hamelberg D., McCammon J. A., (2006). Elasticity of peptide omega bonds. Physical Review E, 73, 041908

  38. Vera C., Lao J., Hamelberg D., Sung L. A., (2005). Mapping the tropomyosin isoform 5 binding site on human erythrocyte tropomodulin: Further insights into E-Tmod/TM5 interaction. Archives of Biochemistry and Biophysics, 444, 130-138 (Cover Issue)

  39. Hamelberg D., McCammon J. A., (2005). Fast Peptidyl cis-trans Isomerization within the Flexible Gly-Rich Flaps of HIV-1 Protease. Journal of the American Chemical Society, 127, 13778-13779

  40. Shen TY, Zong CH, Hamelberg D., McCammon J. A., Wolynes, P. G, (2005). The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB Journal, 19, 1389-1395

  41. Hamelberg D., Shen T., McCammon J. A., (2005). Relating kinetic rates and local energetic roughness byaccelerated molecular-dynamics simulations. Journal of Chemical Physics, 122, 241103

  42. Hamelberg D., Shen T., McCammon J. A., (2005). 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, 1969-1974

  43. Chaires J. B., Ren .J, Hamelberg D., Kumar A., Pandya V., Boykin D. W., Wilson W. D., (2004). Structural selectivity of aromatic diamidines. Journal of Medicinal Chemistry, 47, 5729-5742

  44. Hamelberg D., McCammon J. A., (2004). 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, 7683-7689

  45. Hamelberg, D., Mongan J., McCammon J. A., (2004). Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. Journal of Chemical Physics, 120 (24), 11919-11929

  46. Grossman R., Kasturi, P., Hamelberg, D., Liu, B. (2004). An empirical study of the universal chemical key algorithm for assigning unique keys to chemical compounds. Journal of Bioinformatics and Computational Biology, 2, 155-171

  47. Tanious F. A., Hamelberg D., Bailly C., Czarny, A., Boykin D. W., Wilson, W. D., (2004). DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives. Journal of the American Chemical Society, 126, 143-153

  48. Nguyen B, Hamelberg D., Bailly C., Colson P., Stanek J., Brun R., Neidle S., Wilson W. D. (2004). Characterization of Novel DNA minor-groove complex. Biophysical Journal. 82, 1028-1041

  49. Grossman R. L., Gu Y. H., Hamelberg D., Hanley D., Hong X. W., Levera J., Lillethun D., Mazzucco M., Mambretti J., Weinberger J., (2003). Experimental studies using photonic data services at IGrid 2002. Future Generation Computer Systems 19, 945-955

  50. Nguyen B, Lee M. P. H., Hamelberg D., Joubert A., Bailly C., Brun R., Neidle S., Wilson W. D. (2002). 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

  51. Hamelberg D., Williams, L. D., Wilson, W. D., (2002). The Effect of Neutralized Phosphate Backbone on the Minor Groove Structure of B-DNA: Molecular Dynamics Simulation Studies. Nucleic Acid Research, 30, 3615-3623

  52. Hamelberg D., Williams, L. D., Wilson, W. D., (2001). Influence of the Dynamic Positions of Cations onthe Structure of the DNA Minor: Sequence Dependent Effects. Journal of the American Chemical Society, 123, 7745-7755

  53. Hamelberg D., McFail-Isom, L., Williams, L. D., Wilson, W. D., (2000). Flexible Structure of DNA: Ion Dependence of Minor-Groove Structure and Dynamics. Journal of the American Chemical Society, 122, 10513-10520