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2010

This folder holds the following references to publications, sorted by year and author.

There are 21 references in this bibliography folder.

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Bellesia G, Asztalos A, Shen T, Langan P, Redondo A, and Gnanakaran S (2010).
In Silico Studies of Crystalline Cellulose and Its Degradation by Enzymes.
ACTA Crystallographica. Section D: Biological Crystallography , 66(11):1184-1188.

Berezniak T, Zahran M, Imhof P, Jaeschke A, and Smith JC (2010).
Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme.
Journal of the American Chemical Society, 132(36):12587–12596.

Bondar AN, Smith JC, and Elstner M (2010).
Mechanism of a Proton Pump Analyzed with Computer Simulations.
Theoretical Chemistry Accounts, 125(3-6):353-363.

Daidone I, Neuweiler H, Doose S, Sauer M, and Smith JC (2010).
Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains.
PLoS Computational Biology, 6(1):e1000645.

Glass D, Krishnan M, Nutt D, and Smith JC (2010).
Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models.
Journal of Chemical Theory and Computation, 6(4):1390-1400.

Guan Y, Ranoa DRE, Jiang S, Mutha S, Li X, Baudry J, and Tapping RI (2010).
Human TLRs 10 and 1 Share Common Mechanisms of Innate Immune Sensing but Not Signaling.
The Journal of Immunology, 184(9):5094-5103.

Guo HB, Johs A, Parks JM, Oliff L, Miller SM, Summers AO, Liang L, and Smith JC (2010).
Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg(II).
Journal of Molecular Biology, 398(4):555-568.

Johnson Q, Doshi U, Shen T, and Hamelberg D (2010).
Water’s Contribution to the Energetic Roughness from Peptide Dynamics.
Journal of Chemical Theory and Computation, 6(9):2591-2597.

Lopez M, Kurkal-Siebert V, Dunn RV, Tehei M, Finney JL, Smith JC, and Daniel RM (2010).
Activity and Dynamics of an Enzyme, Pig Liver Esterase, in Near-Anhydrous Conditions.
Biophysical Journal, 99(8):L62-L64.

Lu B, Cheng X, Huang J, and McCammon J (2010).
AFMPB: An Improved Poisson-Boltzmann Solver Using an Adaptive Fast Multipole Method.
Computer Physics Communications, 181(6):1150-1160.

Lynch RM, Rong R, Li B, Shen T, Honnen W, Mulenga J, Allen S, Pinter A, Gnanakaran S, and Derdeyn CA (2010).
Subtype-Specific Conservation of Isoleucine 309 in the Envelope V3 Domain is Linked to Immune Evasion in Subtype C HIV-1 Infection.
Virology, 404(1):59-70.

Moritsugu K, Njunda BM, and Smith JC (2010).
Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding.
Journal of Physical Chemistry B, 114(3):1479–1485.

Parks JM, Imhof P, and Smith JC (2010).
Understanding Enzyme Catalysis Using Computer Simulation.
In: Encyclopedia of Catalysis, ed. by IT Horváth. Wiley, chap. ?, pp. 1-45. (ISBN: 9780471227618).

Saharay M, Guo H, and Smith JC (2010).
Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS.
PLos ONE, 5(10):e12947.

Ulmschneider MB, Doux JPF, Killian JA, Smith JC, and Ulmschneider JP (2010).
Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides.
Journal of the American Chemical Society, 132(10):3452–3460.

Ulmschneider MB, Smith JC, and Ulmschneider JP (2010).
Peptide Partitioning Properties from Direct Insertion Studies.
Biophysical Journal, 98(12):L60-L62.

Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TYS, Martin SL, Guo HB, Smith JC, and Brown SD (2010).
A Paradigm for Strain Improvement Identifies Sodium Acetate Tolerance Loci in Zymomonas mobilis and Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences USA, 107(23):10395-10400.

Zahran M, Daidone I, Smith JC, and Imhof P (2010).
Mechanism of DNA Recognition by the Restriction Enzyme EcoRV.
Journal of Molecular Biology, 401(3):415-432.

 
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