Publications

At Department of Chemistry
Georgia State University

  1. Lee E., Redzic J. S., Sarkar S., Rivkin D., Gordon B., Saviola A. J., Maroney S. P., Thorstenson J. C., Hansen K. C., Horswill A. R., Hamelberg D., Eisenmesser E. Z., (2026). N-terminal processing unlocks global dynamics for substrate engagement in Spl proteases. Science Advances, 12, 1-10

  2. Singh H., Hamelberg D., (2026). Contact Dynamics-based Perturbation Analysis: Revealing Allosteric Communication Pathways in Proteins. Computational Modeling of Biomolecular Interactions: Methods and Applications, Y. Miao (Ed.), Chapter 16, 517-542

  3. Kumutima J., Yao X-Q., Hamelberg D., (2026). Alanine Rewires the Communication Pathways Established During the Allosteric Activation of Liver Pyruvate Kinase by Fructose Bisphosphate. Journal of Chemical Information and Modeling, 66, 6637–6643

  4. Dratch B. D., Ouedraogo D., Ball J., Hamelberg D., Gadda G. (2026). Mechanistic and Molecular Dynamics Studies Reveal that Increased Loop 3 Mobility Alters Substrate Capture in an NADH:Quinone Oxidoreductase. Biochemistry, 65, 104-113

  5. Mulpuri N., Yao X-Q., Hamelberg D., (2025). Uncovering the Role of Distal Regions in PDK1 Allosteric Activation. ACS Bio & Med Chem Au, 5, 299–309

  6. Lee E., Tran N., Redzic J. S., Singh H., Alamillo L., Holyoak T., Hamelberg D., Eisenmesser E. Z., (2025). Identifying and controlling inactive and active conformations of a serine protease. Science Advances, 11, 1-9

  7. Huang G., Singh H., Singh P., Varshnaya R. K., Hamelberg D., Wang B., Docampo R., (2025). Chemical and Genetic Validation of an Essential Calcium Entry Channel of Trypanosoma brucei as a Therapeutic Target. ACS Infectious Diseases, 11, 1741-1752

  8. Lyles K. V., Stone S., Singh P., Patterson L. D., Natekar J., Pathak H., Varshnaya R. K., Elsharkawy A., Liu D., Bansal S., Faniyi O. O., Tang S., Yang X., Mulpuri N., Hamelberg D., Kang C. , Wang B., Kumar M., Luo M., (2025). Entry Inhibitors of SARS-CoV-2 Targeting the Transmembrane Domain of the Spike Protein. Viruses, 17, 989

  9. Yao X-Q., Hamelberg D., (2024). Dissecting the Allosteric Fine-Tuning of Enzyme Catalysis. Journal of the American Chemical Society Au, 4, 837–846

  10. Souffrant M. G., Yao X-Q., Hamelberg D., (2023). Evolving Mutational Buildup in HIV-1 Protease Shifts Conformational Dynamics to Gain Drug Resistance. Journal of Chemical Information and Modeling, 12, 3892–3902

  11. Ahmed F., Yao X-Q., Hamelberg D., (2023). Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins. Journal of Physical Chemistry B, 127, 3139–3150

  12. Ouedraogo D., Souffrant M., Yao X-Q., Hamelberg D., Gadda G. (2023). Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase. Biochemistry, 62, 1070-1081

  13. Sharma N., Setiawan D., Hamelberg D., Narayan R., Aneja R., (2023). Computational benchmarking of putative KIFC1 inhibitors. Medicinal Research Reviews, 43, 293-318

  14. Kumutima J., Yao X-Q., Hamelberg D., (2022). Post-translational Modifications of Cyclophilin D Fine-Tune Its Conformational Dynamics and Activity: Implications for Its Mitochondrial Function. Journal of Physical Chemistry B, 51, 10844–10853

  15. Yao X-Q., Hamelberg D., (2022). From Distinct to Differential Conformational Dynamics to Map Allosteric Communication Pathways in Proteins. Journal of Physical Chemistry B, 126, 2612–2620(Cover Issue)

  16. Yao X-Q., Hamelberg D., (2022). Residue–Residue Contact Changes during Functional Processes Define Allosteric Communication Pathways. Journal of Chemical Theory and Computation, 18, 1173–1187

  17. Deng X., Yao X-Q., Berglund K., Dong B., Ouedrago D., Ghane M. A., Zhuo Y., McBean C., Wei Z. Z., Gozem S., Yu S. P., Wei L., Fang N., Mabb A. M., Gadda G., Hamelberg D., Yang J. J., (2021). Tuning Protein Dynamics to Sense Rapid Endoplasmic‐Reticulum Calcium Dynamics. Angewandte Chemie, 60, 23289-23298

  18. Kumutima J., Yao X-Q., Hamelberg D., (2021). p53 Is Potentially Regulated by Cyclophilin D in the Triple-Proline Loop of the DNA Binding. Biochemistry, 60, 597–606

  19. Dodd T., Yao X-Q., Hamelberg D., Ivanov I., (2021). Subsets of adjacent nodes (SOAN): a fast method for computing suboptimal paths in protein dynamic networks. Molecular Physics, 119, e1893847

  20. Iyer A., Reis R. A. G., Gannavaram S., Momin M., Spring-Connell A. M., Orozco-Gonzalez Y., Agniswamy J., Hamelberg D., Weber I. T., Gozem S., Wang S., Germann M. W., Gadda G. (2021). A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry, 60, 711−724

  21. Essam Z. M., Ozmen G.E., Setiawan D., Hamid R.R., Abd El-Aal R.M., Aneja R., Hamelberg D., Henary M., (2021). Donor acceptor fluorophores: synthesis, optical properties, TD-DFT and cytotoxicity studies Organic & Biomolecular Chemistry, 19, 1835-1846

  22. Souffrant M. G., Yao X-Q., Momin M., Hamelberg D., (2020). N-Glycosylation and Gaucher Disease Mutation Allosterically Alter Active-Site Dynamics of Acid-β-Glucosidase. ACS Catalysis, 10, 1810-1820

  23. Deng X., Xin Y., Miller C. L., Hamelberg D., Kirberger M., Moremen K. W., Hu J., Yang J. J., (2020). Structural mechanism of cooperative regulation of calcium-sensing receptor-mediated cellular signaling. Current Opinion in Physiology, 17, 269-277

  24. Yao X-Q., Hamelberg D., (2019). Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis. Accounts of Chemical Research, 52, 3455-3464

  25. Childers K. C., Yao X-Q., Giannakoulias S., Amason J., Hamelberg D., Garcin E. D., (2019). Synergistic mutations in soluble guanylyl cyclase (sGC) reveal a key role for interfacial regions in the sGC activation mechanism. Journal of Biological Chemistry, 294, 18451–18464

  26. Yao X-Q., Momin M., Hamelberg D., (2019). Establishing a Framework of Using Residue–Residue Interactions in Protein Difference Network Analysis. Journal of Chemical Information and Modeling, 59, 3222-3228

  27. Owens E. A., Huynh H. T, Stroeva E. M., Barman A., Ziabrev K., Paul A., Nguyen S. V., Laramie M., Hamelberg D., Germann M. W., Wilson W. D., Henary M., (2019). Second Generation G-Quadruplex Stabilizing Trimethine Cyanines Bioconjugate Chemistry, 30, 2647-2663

  28. Ho K. C., Hamelberg D., (2018). Combinatorial Coarse-Graining of Molecular Dynamics Simulations for Detecting Relationships between Local Configurations and Overall Conformations. Journal of Chemical Theory and Computation, 14, 6026–6034

  29. Yao X-Q., Momin M., Hamelberg D., (2018). Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis. Journal of Chemical Information and Modeling, 58, 1325-1330

  30. Rodriguiz-Bussey I., Yao X-Q., Shouaib A. D., Lopez J., Hamelberg D., (2018). Decoding Allosteric Communication Pathways in Cyclophilin A with a Comparative Analysis of Perturbed Conformational Ensembles. Journal of Physical Chemistry B, 122, 6528-6535

  31. Momin M., Yao X-Q., Thor W., Hamelberg D., (2018). Substrate Sequence Determines Catalytic Activities, Domain-Binding Preferences, and Allosteric Mechanisms in Pin1. Journal of Physical Chemistry B, 122, 6521-6527

  32. Vu P. J., Yao XQ., Momin M., Hamelberg D., (2018). Unraveling Allosteric Mechanisms of Enzymatic Catalysis with an Evolutionary Analysis of Residue–Residue Contact Dynamical Changes. ACS Catalysis, 8, 2375–2384

  33. Adeniran C., Hamelberg D., (2017). Redox-Specific Allosteric Modulation of the Conformational Dynamics of κB DNA by Pirin in the NF-κB Supramolecular Complex. Biochemistry, 56, 5002–5010

  34. Robbins J. M., Souffrant M., Hamelberg D., Gadda G., Bommarius A. S. (2017). Enzyme-Mediated Conversion of Flavin Adenine Dinucleotide (FAD) to 8-Formyl FAD in Formate Oxidase Results in a Modified Cofactor with Enhanced Catalytic Properties. Biochemistry, 56, 3800−3807

  35. Momin M., Xin Y., Hamelberg D., (2017). Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective. Journal of Physical Chemistry B, 121, 6131−6138

  36. Ouedraogo D., Souffrant M., Vasquez S., Hamelberg D., Gadda G. (2017). Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry, 56, 2477−2487

  37. Barman A., Hamelberg D., (2016). Fe(II)/Fe(III) Redox Process Can Significantly Modulate the Conformational Dynamics and Electrostatics of Pirin in NF-κB Regulation. ACS Omega, 1, 837−842

  38. Doshi U., Holliday M. J., Eisenmesser E. Z., Hamelberg D., (2016). 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, 4735–4740

  39. Barman A., Hamelberg D., (2016). Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1. Journal of Physical Chemistry B, 120, 8405−8415

  40. Barman A., Smitherman C., Souffrant M., Gadda G., Hamelberg D., (2016). Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. Journal of Chemical Information and Modeling, 56, 139-147

  41. Elvira Romero, Safieh Tork Ladani, Hamelberg D., Gadda G. (2016). Solvent-Slaved Motions in the Hydride Tunneling Reaction Catalyzed by Human Glycolate Oxidase. ACS Catalysis, 6, 2113-2120

  42. Ho K. C., Hamelberg D., (2016). Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation. Journal of Chemical Theory and Computation, 12, 372–382

  43. Francesca Salvi, Isela Rodriguez, Hamelberg D., Gadda G. (2016). Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase. Biochemistry, 55, 1473-1484

  44. Rodriguez-Bussey I. G., Doshi U., Hamelberg D., (2016). Enhanced molecular dynamics sampling of drug target conformations. Biopolymers, 105, 35-42

  45. Tork-Ladani S., Souffrant M. G.,Barman A., Hamelberg D., (2015). Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases. Biochimica et Biophysica ACTA-General Subjects, 1850, 1994-2004

  46. Barman A., Batiste B., Hamelberg D., (2015). Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH-pi Interactions in Proteins. Journal of Chemical Theory and Computation, 11, 1854-1863

  47. Liu F. G., Geng J. F., Gumpper R. H., Barman A., Davis I., Ozarowski A., Hamelberg D., Liu A. M. , (2015). An Iron Reservoir to the Catalytic Metal: The Rubredoxin Iron In An Extradiol Dioxygenase. Journal of Biological Chemistry, 290, 15621-15634

  48. Mishra R. C., Gundala S. R., Karna P., Lopus M., Gupta K. K., Nagaraju M., Hamelberg D., Tandon V., Panda D., Reid M. D., Aneja R., (2015). Design, synthesis and biological evaluation of di-substituted noscapine analogs as potent and microtubule-targeted anticancer agents. Bioorganic & Medicinal Chemistry Letters, 25, 2133-2140

  49. Velazquez H. A., Hamelberg D., (2015). Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations. Journal of Chemical Physics, 142, 075102

  50. Doshi U., Hamelberg D., (2015). Towards fast, rigorous and efficient conformational sampling of biomolecules: advances in Accelerated Molecular Dynamics. Biochimica et Biophysica Acta (BBA) - General Subjects, 1850, 878-888

  51. Barman A., Hamelberg D., (2015). Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis–tau peptide. Proteins: Structure, Function, and Bioinformatics, 83, 436–444

  52. Barman A., Hamelberg D., (2014). Cysteine-Mediated Dynamic Hydrogen-Bonding Network in the Active Site of Pin1. Biochemistry, 53, 3839–3850

  53. Tork-Ladani S., Hamelberg D., (2014). Intricacies of interactions, dynamics and solvent effects in enzyme catalysis: a computational perspective on cyclophilin A. Molecular Simulation, 40, 765-776

  54. Doshi U., Hamelberg D., (2014). Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent. Journal of Physical Chemistry Letters, 5, 1217–1224

  55. Madan J., Gundala S. R., Baruah B., Nagaraju M., Yates C., Turner T., Rangari V., Hamelberg D., Reid M. D., Aneja R., (2014). Cyclodextrin Complexes of Reduced Bromonoscapine in Guar Gum Microspheres Enhance Colonic Drug Delivery. Molecular Pharmaceutics, 11, 4339-4349

  56. Zhang C., Mulpuri N., Hannan F. M., Nesbit M. A., Thakker R. V., Hamelberg D., Brown E. M., Yang J. J., (2014). Role of Ca2+ and L-Phe in Regulating Functional Cooperativity of Disease-Associated "Toggle" Calcium-Sensing Receptor Mutations. PLoS ONE, 11, e113622

  57. Henary M., Narayanaa L., Ahad S., Gundala S. R., Mukkavilli R., Sharma V., Owens E. A., Yadav Y., Nagaraju M., Hamelberg D.,Tandon V., Panda D., Aneja R., (2014). Novel third-generation water-soluble noscapine analogs as superior microtubule-interfering agents with enhanced antiproliferative activity. Biochemical Pharmacology, 92, 192–205

  58. Zhang C., Huang Y., Jiang Y., Mulpuri N., Wei L., Hamelberg D., Brown E. M., Yang J. J., (2014). Identification of an L-Phenylalanine Binding Site Enhancing The Cooperative Responses of The Calcium Sensing Receptor to Calcium. Journal of Biological Chemistry, 289, 5296-5309

  59. Jiang J. Y., Nagaraju M., Meyer R. C., Zhang L., Hamelberg D., Hall R. A., Brown E. M., Conn P. J., Yang J. J. (2014). Extracellular calcium modulates actions of orthosteric and allosteric ligands on metabotropic glutamate receptor 1α. Journal of Biological Chemistry, 289, 1649-1661

  60. Levitz A., Tork-Ladani S., Hamelberg D., Henary M., (2014). Synthesis and effect of heterocycle modification on the spectroscopic properties of a series of unsymmetrical trimethine cyanine dyes. Dyes and Pigments, 105, 238–249

  61. Doshi U., Hamelberg D., (2014). The Dilemma of Conformational Dynamics in Enzyme Catalysis: Perspectives from Theory and Experiment. in Protein Conformational Dynamics: Advances in Experimental Medicine and Biology, Han, K.-l.; Zhang, X.; Yang, M.-j., Eds. Springer International Publishing, 805, 221-243

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

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

  78. 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

  79. 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

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

  81. 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

  82. 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

  83. 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

  84. 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

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

  86. 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

  87. 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

  88. 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)

  89. 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

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

  91. 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

  92. 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

  93. 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

  94. 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)

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

  96. 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

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

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

  99. 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)

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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

  113. 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

  114. 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