Publications

At Department of Chemistry
Georgia State University

  1. 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

  2. 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

  3. 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

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

  5. 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

  6. 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)

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

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

  31. 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

  32. 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

  33. 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

  34. 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

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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

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

  44. 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

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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

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

  69. 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

  70. 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

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

  72. 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

  73. 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

  74. 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

  75. 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

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

  77. 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

  78. 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

  79. 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)

  80. 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

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

  82. 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

  83. 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

  84. 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

  85. 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)

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

  87. 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

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

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

  90. 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)

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

  105. 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