Publications
This folder holds the following references to publications, sorted by year and author.
There are 64 references in this bibliography folder.
Bondar AN, and Smith JC (in press).
Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping.
Israel Journal of Chemistry.
Krishnan M, and Smith JC (in press).
Response of Small-Scale, Methyl Rotors to Protein-Ligand Association: A Simulation Analysis of Calmodulin-Peptide Binding.
Journal of the American Chemical Society.
Lu B, Cheng X, Huang J, and McCammon JA (in press).
An Improved Poisson-Boltzmann Solver Using an Adaptive Fast Multipole Method.
Journal of Chemical Theory and Computation.
Petridis L, Xu J, Crowley M, Smith JC, and Cheng X (in press).
Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes.
Biofuels: ACS.
Saharay M, Guo HB, Smith JC, and Guo H (in press).
QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates. .
Biofuels: ACS.
Spies A, Reese JG, Dodd D, Pankow K, Blanke S, and Baudry J (in press).
Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase.
Journal of the American Chemical Society.
Cheng X, Ivanov I, Wang HL, Sine SM, and McCammon JA (2009).
Molecular Dynamics Simulations of a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor.
Biophysical Journal, 96(11).
Guo H, 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.
Moritsugu K, and Smith JC (2009).
REACH: A Program for Coarse-Grained Biomolecular Simulation.
Computer Physics Communications.
Schulz R, Krishnan M, Daidone I, and Smith JC (2009).
Instantaneous Normal Modes and the Protein Glass Transition.
Biophysical Journal, 96(2):476–484.
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.
Becker V, Sengupta D, Ketteler R, Ullmann MG, Smith JC, and Klingmüller U (2008).
Packing Density of the Erythropoietin Receptor Transmembrane Domain Correlates with Amplification of Biological Responses.
Biochemistry, 47(45):11771–11782.
Bondar AN, Baudry J, Suhai S, Fischer S, and Smith JC (2008).
Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions.
Journal of Physical Chemistry B, 112(47):14729–14741.
Krishnan M, Kurkal-Siebert V, and Smith JC (2008).
Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin.
Journal of Physical Chemistry B, 112(17):5522-5533.
Kurkal-Siebert V, Agarwal R, and Smith JC (2008).
Hydration-Dependent Dynamical Transition in Protein: Protein Interactions at Approximately 240 K.
Physical Review Letters, 100(13):138102.
McLain S, Soper A, Daidone I, Smith J, and Watts A (2008).
Charge-Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution.
Angewandte Chemie International Edition, 120(47):9199–9202.
Meinhold L, Clement D, Tehei M, Daniel R, Finney JL, and Smith JC (2008).
Protein Dynamics and Stability: The Distribution of Atomic Fluctuations in Thermophilic and Mesophilic Dihydrofolate Reductase Derived Using Elastic Incoherent Neutron Scattering.
Biophysical Journal, 94(12):4812–4818.
Moritsugu K, and Smith JC (2008).
REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes.
Biophysical Journal, 95(4):1639–1648.
Neusius T, Daidone I, Sokolov IM, and Smith JC (2008).
Subdiffusion in Peptides Originates from the Fractal-Like Structure of Configuration Space.
Physical Review Letters, 100(18):188103.
Noé F, Daidone I, Smith JC, di Nola A, and Amadei A (2008).
Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation.
Journal of Physical Chemistry B, 112(35):11155-11163.
Nutt DR, and Smith JC (2008).
Dual Function of the Hydration Layer around an Antifreeze Protein Revealed by Atomistic Molecular Dynamics Simulations.
Journal of the American Chemical Society, 130(39):13066-13073.
Petridis L, and Smith JC (2008).
Cellulosic Ethanol: Progress towards a Simulation Model of Lignocellulosic Biomass.
Journal of Physics: Conference Series, 125(1):012055.
Petridis L, and Smith JC (2008).
A Molecular Mechanics Force Field for Lignin.
Journal of Computational Chemistry, 30(3):457-467.
Sengupta D, Smith JC, and Ullmann GM (2008).
Partitioning of Amino-Acid Analogues in a Five-Slab Membrane Model.
Biochimica et Biophysica Acta, 1778(10):2234–2243.
Splettstoesser T, Noé F, Oda T, and Smith JC (2008).
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.
