2007
This folder holds the following references to publications, sorted by year and author.
There are 19 references in this bibliography folder.
Bondar A, Suhai S, Fischer S, Smith J, 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 A, Suhai S, Smith J, 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 M, and Smith J (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 M, Di Nola A, Amadei A, and Smith J (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 J, 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 J, 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, and Smith J (2007).
Protein Dynamics from X-Ray Crystallography: Anisotropic, Global Motion in Diffuse Scattering Patterns.
Proteins, 66(4):941–953.
Meinhold L, Merzel F, and Smith J (2007).
Lattice Dynamics of a Protein Crystal.
Physical Review Letters, 99(13):138101.
Meinhold L, Smith J, Kitao A, and Zewail A (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 J, 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 J (2007).
Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian.
Biophysical Journal, 93(10):3460–3469.
Noé F, and Smith J (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 J (2007).
Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States.
Journal of Chemical Physics, 126(15):155102.
Nutt D, and Smith J (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 D, and Smith J (2007).
Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?
Journal of Chemical Theory and Computation, 3(4):1550–1560.
Topham C, and Smith J (2007).
Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form.
Biophysical Journal, 92(3):769–786.
Xu Q, Guo H, 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.
