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2007

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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Bondar AN, Suhai S, Fischer S, Smith JC, and Elstner M (2007).
Suppression of the Back Proton-Transfer from Asp85 to the Retinal Schiff Base in Bacteriorhodopsin: A Theoretical Analysis of Structural Elements.
Journal of Structural Biology, 157(3):454–469.

Bondar AN, Suhai S, Smith JC, and Frangopol P (2007).
Computer Simulations of Local Anesthetic Mechanisms: Quantum Chemical Investigation of Procaine.
Romanian Reports in Physics, 59(2):289-299.

Cournia Z, Ullmann MG, and Smith JC (2007).
Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine Membrane: A Molecular Dynamics Simulation Study.
Journal of Physical Chemistry B, 111(7):1786–1801.

Daidone I, Ulmschneider MB, Di Nola A, Amadei A, and Smith JC (2007).
Dehydration-Driven Solvent Exposure of Hydrophobic Surfaces as a Driving Force in Peptide Folding.
Proceedings of the National Academy of Sciences USA, 104(39):15230–15235.

de Hatten X, Cournia Z, Huc I, Smith JC, and Metzler-Nolte N (2007).
Force-Field Development and Molecular Dynamics Simulations of Ferrocene-Peptide Conjugates as a Scaffold for Hydrogenase Mimics.
Chemistry - A European Journal, 13(29):8139–8152.

Guo HB, and Guo H (2007).
Mechanism of Histone Methylation Catalyzed by Protein Lysine Methyltransferase SET7/9 and Origin of Product Specificity.
Proceedings of the National Academy of Sciences USA, 104(21):8797–8802.

Koppole S, Smith JC, and Fischer S (2007).
The Structural Coupling between ATPase Activation and Recovery Stroke in the Myosin II Motor.
Structure, 15(7):825–837.

Meinhold L, Merzel F, and Smith JC (2007).
Lattice Dynamics of a Protein Crystal.
Physical Review Letters, 99(13):138101.

Meinhold L, Smith JC, Kitao A, and Zewail AH (2007).
Picosecond Fluctuating Protein Energy Landscape Mapped by Pressure Temperature Molecular Dynamics Simulation.
Proceedings of the National Academy of Sciences USA, 104(44):17261–17265.

Mesentean S, Koppole S, Smith JC, and Fischer S (2007).
The Principal Motions Involved in the Coupling Mechanism of the Recovery Stroke of the Myosin Motor.
Journal of Molecular Biology, 367(2):591–602.

Moritsugu K, and Smith JC (2007).
Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian.
Biophysical Journal, 93(10):3460–3469.

Noé F, and Smith JC (2007).
Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science.
In: Mathematical Modeling of Biological Systems, Volume I, ed. by A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel, chap. 11, pp. 121–137, Birkhäuser Boston. (ISBN: 978-0-8176-4557-1 (Print) 978-0-8176-4558-8 (Online)).

Noé F, Horenko I, Schütte C, and Smith JC (2007).
Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States.
Journal of Chemical Physics, 126(15):155102.

Nutt DR, and Smith JC (2007).
Choosing an Appropriate Water Model for Use in Biomolecular Simulations.
In: Physics and Chemistry of Ice, ed. by Kuhs, W. F., pp. 451-458, RSC Publishing.

Nutt DR, and Smith JC (2007).
Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?
Journal of Chemical Theory and Computation, 3(4):1550–1560.

Xu Q, Guo HB, Gorin A, and Guo H (2007).
Stabilization of a Transition-State Analogue at the Active Site of Yeast Cytosine Deaminase: Importance of Proton Transfers.
Journal of Physical Chemistry B, 111(23):6501–6506.

Xu Q, Guo HB, Wlodawer A, Nakayama T, and Guo H (2007).
The QM/MM Molecular Dynamics and Free Energy Simulations of the Acylation Reaction Catalyzed by the Serine-Carboxyl Peptidase Kumamolisin-As.
Biochemistry, 46(12):3784–3792.

 
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