This folder holds the following references to publications, sorted by year and author.
There are 23 references in this bibliography folder.
Bondar AN, and Smith JC (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 HL, Sine SM, and McCammon JA (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 JC (2009).
Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis.
Krishnan M, and Smith JC (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 JC (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 JC (2009).
REACH: A Program for Coarse-Grained Biomolecular Simulation.
Computer Physics Communications, 180(7):1188-1195.
Moritsugu K, Kurkal-Siebert V, and Smith JC (2009).
REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics.
Biophyical Journal, 97(4):1158-1167.
Neusius T, Sokolov IM, and Smith JC (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 JC (2009).
A Molecular Mechanics Force Field for Lignin.
Journal of Computational Chemistry, 30(3):457-467.
Phatak P, Fraemcke JS, Wanko M, Hoffmann M, Strodel P, Smith JC, Suhai S, Bondar AN, 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 JC (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.
Shen T, Langan P, French A, Johnson GP, and Gnanakaran S (2009).
Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence.
Journal of the American Chemical Society, 131(41):14786–14794.
Smith JC (2009).
Supercomputers Tackle Biofuel Production Problems.
Spies A, Reese JG, Dodd D, Pankow KL, Blanke SR, 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 JC (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.
Thukral L, Smith JC, and Daidone I (2009).
Common Folding Mechanism of a Beta-Hairpin Peptide via Non-Native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations.
Journal of the American Chemical Society, 131(50):18147–18152.
Ulmschneider JP, Smith JC, Killian A, and Ulmschneider MB (2009).
Peptide Partitioning and Folding into Lipid Bilayers.
Journal of Chemical Theory and Computation, 5(9):2202-2205.
Xu J, Crowley MF, and Smith JC (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.
Xu Q, Chu Y, Guo HB, Smith JC, and Guo H (2009).
Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free Energy Simulations of Protein Lysine Methyltransferases.
Chemistry: A European Journal, 15(46):12596-12599.
Xu Q, Ye X, Li LY, Cheng ZM, and Guo H (2009).
Structural Basis for the Action of Xyloglucan Endotransglycosylases/hydrolases: Insights from Homology Modeling.
Interdisciplinary Sciences: Computational Life Sciences, 2(2):133-139.