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

There are 19 references in this bibliography folder.

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Balog E, Smith JC, and Perahia D (2006).
Conformational Heterogeneity and Low-Frequency Vibrational Modes of Proteins.
Physical Chemistry Chemical Physics, 8:5543-5548.

Baudry J (2006).
Van der Waals Interactions and Decrease of the Rotational Barrier of Methyl-size Rotators: A Theoretical Study.
Journal of the American Chemical Society, 128(34):11088-11093.

Bondar AN, Smith JC, and Fischer S (2006).
Structural and Energetic Determinants of Proton Transfer in Bacteriorhodopsin.
Photochemical and Photobiological Sciences, 5:547-552.

Efferth T, Schwarzl SM, Smith JC, and Osieka R (2006).
Role of Glucose-6-Phosphate Dehydrogenase for Oxidative Stress and Apoptosis.
Cell Death and Differentiation, 13:527-528.

Guo H, Wlodawer A, Nakayama T, Xu Q, and Guo H (2006).
Catalytic Role of Proton Transfers in the Formation of a Tetrahedral Adduct in a Serine Carboxyl Peptidase.
Biochemistry, 45(30):9129–9137.

Imhof P, Noé F, Fischer S, and Smith JC (2006).
AM1/d Parameters for Magnesium in Metalloenzymes.
Journal of Chemical Theory and Computation, 2(4):1050–1056.

Koppole S, Smith JC, and Fischer S (2006).
Simulations of the Myosin II Motor Reveal a Nucleotide-State Sensing Element that Controls the Recovery Stroke.
Journal of Molecular Biology, 361(3):604-616.

Kurkal-Siebert V, and Smith JC (2006).
Low-Temperature Protein Physics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K.
Journal of the American Chemical Society, 128(7):2356-2364.

Kurkal-Siebert V, Daniel R, Finney JL, Tehei M, Dunn RV, and Smith JC (2006).
Enzyme Hydration, Activity and Flexibility: A Neutron Scattering Approach.
Journal of Noncrystalline Solids, 352(42-49):4387-4393.

Mesentean S, Fischer S, and Smith JC (2006).
Analyzing Large-Scale Structural Change in Proteins: Comparison of Principal Component Projection and Sammon Mapping.
Proteins: Structure, Function and Bioinformatics, 64(1):210-218.

Moritsugu K, and Smith JC (2006).
Temperature-Dependent Protein Dynamics: A Simulation-Based Probabilistic Diffusion-Vibration Langevin Description.
The Journal of Physical Chemistry B, 110(11):5807–5816.

Noé F, Krachtus D, Smith JC, and Fischer S (2006).
Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins.
Journal of Chemical Theory and Computation, 2(3):840-857.

Noé F, Oswald M, Reinelt G, Fischer S, and Smith JC (2006).
Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the αL ↔ β ↔ αR Transitions in Octaalanine.
Journal of Multiscale Modelling and Simulation, 5(2):393-419.

Schwarzl SM, Smith JC, and Fischer S (2006).
Insights into the Chemomechanical Coupling of the Myosin Motor from Simulation of its ATP Hydrolysis Mechanism.
Biochemistry, 45(18):5830-5847.

Smith JC (2006).
Tight in Titin.
Structure, 14(3):389-390.

Smith JC, Becker T, Fischer S, Noé F, Tournier AL, Ullmann GM, and Kurkal V (2006).
Physical and Functional Aspects of Protein Dynamics.
In: Soft Condensed Matter Physics in Molecular and Cell Biology, ed. by W.C.K. Poon and D. Andelman. Taylor & Francis, chap. 12, pp. 225-241. (ISBN: 978-0750310239).

Tehei M, Smith JC, Monk C, Ollivier J, Öttl M, Kurkal V, Finney JL, and Daniel RM (2006).
Dynamics of Immobilized and Native Escherichia coli Dihydrofolate Reductase by Quasieleastic Neutron Scattering.
Biophysical Journal, 90(3):1090-1097.

Walewski L, Krachtus D, Fischer S, Smith JC, Bala P, and Lesyng B (2006).
SCC-DFTB Energy Barriers for Single and Double Proton Transfer Processes in the Model Molecular Systems Malonaldehyde and Porphycene.
International Journal of Quantum Chemistry, 106(3):636-640.

Xu Q, Guo HB, Wlodawer A, and Guo H (2006).
The Importance of Dynamics in Substrate-Assisted Catalysis and Specificity.
Journal of the American Chemical Society, 128(18):5994–5995.

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