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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
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