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2011

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

There are 44 references in this bibliography folder.

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Balog E, Perahia D, Smith JC, and Merzel F (2011).
Vibrational Softening of a Protein on Ligand Binding.
The Journal of Physical Chemistry B, 115(21):6811-6817.

Biswas M, Voltz K, Smith JC, and Langowski J (2011).
Role of Histone Tails in Structural Stability of the Nucleosome.
PLoS Computational Biology, 7(12): e1002279.

Bondar AN, Fischer S, and Smith JC (2011).
Water Pathways in the Bacteriorhodopsin Proton Pump .
Journal of Membrane Biology, 239(1-2):73-84.

Bondar AN, Knapp-Mohammady M, Suhai S, Fischer S, and Smith JC (2011).
Ground-State Properties of the Retinal Molecule: from Quantum Mechanical to Classical Mechanical Computations of Retinal Proteins.
Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 130(4-6):1169-1183.

Brown SD, Guss AM, Karpinets TV, Parks JM, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwand A, Rodriguez M, Raman B, Shao X, Mielenz JR, Smith JC, Keller M, and Lynd LR (2011).
Mutant Alcohol Dehydrogenase Leads to Improved Ethanol Tolerance in Clostridium thermocellum.
Proceedings of the National Academy of Sciences (U.S.A.), 108(33):13752-13757.

Collignon B, Schulz R, Smith JC, and Baudry J (2011).
Task-Parallel MPI Implementation of Autodock4 for Docking of Very Large Databases of Compounds Using High Performance Super-Computers.
Journal of Computational Chemistry, 32(6):1202-1209.

Daidone I, Di Nola A, and Smith JC (2011).
Molecular Origin of Gerstmann-Sträussler-Scheinker Syndrome: Insight from Computer Simulation of an Amyloidogenic Prion Peptide.
Biophysical Journal, 100(12):3000-3007.

Ellingson SR, and Baudry J (2011).
High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud.
In: Proceedings of the second international workshop on Emerging computational methods for the life sciences, ed. by ECMLS '11. ACM, chap. 5, pp. 33-38. (ISBN: 978-1-4503-0702-4).

Fritsch S, Ivanov I, Wang H, and Cheng X (2011).
Ion Selectivity Mechanism in a Bacterial Pentameric Ligand-Gated Ion Channel.
Biophysical Journal, 100(2):390-398.

Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Andrew Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, and Korber B (2011).
Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections.
PLOS Pathogens, 7(9): e1002209.

Godec A, Smith JC, and Merzel F (2011).
Increase of both Order and Disorder in the First Hydration Shell with Increasing Solute Polarity.
Physical Review Letters, 107(26):267801.

Guo HB, Parks JM, Johs A, and Smith JC (2011).
Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage.
In: Modeling of Molecular Properties, ed. by Peter Comba. Wiley, chap. 20, pp. 311-324.

Hembree W, and Baudry J (2011).
Three-dimensional Mapping of Micro-environmental Control of Methyl Rotational Barriers.
Journal of Physical Chemistry B, 115(26):8575-8580.

Hong L, Lindner B, Smolin N, Sokolov A, and Smith JC (2011).
Three Classes of Motion in the Dynamic Neutron-Scattering Susceptibility of a Globular Protein.
Physical Review Letters, 107(14):148102.

Hu X, Elghobashi-Meinhardt N, Gembris D, and Smith JC (2011).
Response of Water to Electric Fields at Temperatures Below the Glass Transition: A Molecular Dynamics Analysis.
Journal of Chemical Physics, 135:134507.

Hu X, Norris A, Baudry J, and Serpersu E (2011).
Coenzyme A Binding to the Aminoglycoside Acetyltransferase (3)-IIIb Increases Conformational Sampling of Antibiotic Binding Site.
Biochemistry, 50(48):10559-10565.

Johs A, Harwood IM, Parks JM, Nauss RE, Smith JC, Liang L, and Miller SM (2011).
Structural Characterization of Intramolecular Hg2+ Transfer between Flexibly Linked Domains of Mercuric Ion Reductase.
Journal of Molecular Biology, 413 (3):639–656.

Klein H, Cheng X, Smith JC, and Shen T (2011).
Transfer Matrix Approach to the Hydrogen-Bonding in Cellulose Ia Fibrils Describes the Recalcitrance to Thermal Deconstruction.
Journal of Physical Chemistry, 135(8):085106.

Li L, Jiang X, Guan H, Wang P, and Guo H (2011).
Three Alginate Lyases from Marine Bacterium Pseudomonas fluorescens HZJ216: Purification and Characterization.
Applied Biochemistry and Biotechnology, 164(3):305-317.

Miao Y, and Baudry J (2011).
Active Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process.
Biophysical Journal, 101(6):1493-1503.

Mostofian B, Smith JC, and Cheng X (2011).
The Solvation Structures of Cellulose Microfibrils in Ionic Liquids.
Interdisciplinary Sciences - Computational Life Sciences, 3(4):308-320.

Neusius T, Daidone I, Sokolov I, and Smith JC (2011).
Configurational Subdiffusion of Peptides: A Network Study.
Physical Review E, 83:021902.

Noe F, Doose S, Daidone I, Lollmann M, Sauer M, Chodera JD, and Smith JC (2011).
Dynamical Fingerprints: Probing Individual Relaxation Processes in Biomolecular Dynamics with Simulations and Kinetic Experiments.
Proceedings of the National Academy of Sciences (U.S.A), 108(12):4822-4827.

Petridis L, Pingali SV, Urban V, Heller W, O' Neil H, Foston M, Ragauskas A, and Smith JC (2011).
Self-Similar Multiscale Structure of Lignin Revealed by Neutron Scattering and Molecular Dynamics Simulation.
Physical Review E, 83:061911.

 
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