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)

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

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

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

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

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

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)

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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