2009
This folder holds the following references to publications, sorted by year and author.
There are 17 references in this bibliography folder.
Bondar A, and Smith J (2009).
Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping.
Israel Journal of Chemistry, 49(2):155-161.
Cheng X, Ivanov I, Wang H, Sine S, and McCammon J (2009).
Molecular-Dynamics Simulations of ELIC - a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor.
Biophysical Journal, 96(11):4502-4513.
Guo HB, Gorin A, and Guo H (2009).
A Peptide-Linkage Deletion Procedure for Estimate of Energetic Contributions of Individual Peptide Groups in a Complex Environment: Application to Parallel β-Sheets.
Interdisciplinary Sciences: Computational Life Sciences, 1(1):12–20.
Imhof P, Fischer S, and Smith J (2009).
Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis.
Biochemistry, 48(38):9061-9075.
Krishnan M, and Smith J (2009).
Response of Small-Scale, Methyl Rotors to Protein-Ligand Association: A Simulation Analysis of Calmodulin-Peptide Binding.
Journal of the American Chemical Society, 131(29):10083-10091.
Krishnan M, Schulz R, and Smith J (2009).
Protein Dynamical Transition: Role of Methyl Dynamics and Local Diffusion.
Theory and Applications of Computational Chemistry 2008. AIP Conference Proceedings, 1102:122-131.
Moritsugu K, and Smith J (2009).
REACH: A Program for Coarse-Grained Biomolecular Simulation.
Computer Physics Communications, 180(7):1188-1195.
Moritsugu K, Kurkal-Siebert V, and Smith J (2009).
REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics.
Biophyical Journal, 97(4):1158-1167.
Neusius T, Sokolov I, and Smith J (2009).
Subdiffusion in Time-Averaged, Confined Random Walks.
Physical Review E, 80:011109.
Parks JM, Guo H, Momany C, Liang L, Miller SM, Summers AO, and Smith JC (2009).
Mechanism of Hg−C Protonolysis in the Organomercurial Lyase MerB.
Journal of the American Chemical Society, 131(37):13278-13285.
Petridis L, and Smith J (2009).
A Molecular Mechanics Force Field for Lignin.
Journal of Computational Chemistry, 30(3):457-467.
Phatak P, Fraemcke J, Wanko M, Hoffmann M, Strodel P, Smith J, Suhai S, Bondar A, and Elstner M (2009).
Long-Distance Proton Transfer with a Break in the Bacteriorhodopsin Active Site.
Journal of the American Chemical Society, 131(20):7064-7078.
Schulz R, Krishnan M, Daidone I, and Smith J (2009).
Instantaneous Normal Modes and the Protein Glass Transition.
Biophysical Journal, 96(2):476–484.
Schulz R, Lindner B, Petridis L, and Smith JC (2009).
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.
Journal of Chemical Theory and Computation, 5(10):2798-2808.
Spies A, Reese J, Dodd D, Pankow K, Blanke S, and Baudry J (2009).
Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase.
Journal of the American Chemical Society, 131(14):5274-5284.
Splettstoesser T, Noé F, Oda T, and Smith J (2009).
Nucleotide-Dependence of G-Actin Conformation from Multiple Molecular Dynamics Simulations and Observation of a Putatively Polymerization-Competent Superclosed State.
Proteins: Structure, Function, and Bioinformatics, 76(2):353-364.
Xu J, Crowley M, and Smith J (2009).
Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation.
Protein Science, 18(5):949–959.
