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2014

This folder holds the following references to publications, sorted by year and author.

There are 33 references in this bibliography folder.

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Alekozai E, GhattyVenkataKrishna PK, Uberbacher EC, Crowley MF, Smith JC, and Cheng X (2014).
Simulation Analysis of the Cellulase Cel7A Carbohydrate Binding Module on the Surface of the Cellulose Iβ.
Cellulose, 21(2):951-971.

Cashman DJ, Zhu T, Simmerman RF, Scott C, Bruce BD, and Baudry J (2014).
Molecular Interactions between Photosystem I and Ferredoxin: An Integrated Energy Frustration and Experimental Model.
Journal of Molecular Recognition, 27(20):597-608.

Ellingson S, and Baudry J (2014).
High-Throughput Virtual Molecular Docking with AutoDockCloud.
Concurrency and Computation: Practice and Experience , 26(4):907-916.

Ellingson S, Smith JC, and Baudry J (2014).
Polypharmacology and Supercomputer-Based Docking: Opportunities and Challenges.
Molecular Simulation, 40(10-11):848-854.

Ellingson SR, Dakshanamurthy S, Brown M, Smith JC, and Baudry J (2014).
Accelerating Virtual High-Throughput Ligand Docking: Screening One Million Compounds Using a Petascale Supercomputer.
Concurrency and Computation: Practice and Experience, 26(6):1268-1277.

Erler J, Zhang R, Petridis L, Cheng X, Smith JC, and Langowski J (2014).
The Role of Histone Tails in the Nucleosome: A Computational Study.
Biophysical Journal, 107(12):2911-2922.

Esposito EX, Stouch TR, Wymore T, and Madura JD (2014).
Exploring the Physicochemical Properties of Oxime-Reactivation Therapeutics for Cyclosarin, Sarin, Tabun, and VX Inactivated Acetylcholinesterase.
Chemical Research in Toxicology, 27(1):99-110.

Field MJ, and Wymore TW (2014).
Multiscale Modeling of Nerve Agent Hydrolysis Mechanisms: a Tale of Two Nobel Prizes.
Physica Scripta, 89(10):108004.

Harris BJ, Cheng X, and Frymier P (2014).
All-Atom Molecular Dynamics Simulation of a Photosystem I/Detergent Complex.
The Journal of Physical Chemistry B, 118(40):11633–11645.

Harris JB, Eldridge ML, Sayler G, Menn FM, Layton AC, and Baudry J (2014).
A Computational Approach Predicting CYP450 Metabolism and Estrogenic Activity of an Endocrine Disrupting Compound (PCB-30).
Environmental Toxicology and Chemistry, 33(7):1615-1623.

Hong L, Petridis L, and Smith JC (2014).
Biomolecular Structure and Dynamics with Neutrons: The View from Simulation.
Israel Journal of Chemistry, 54(8-9):1264-1273.

Hong L, Sharp MA, Poblete S, Biehl R, Zamponi M, Szekely N, Appavou MS, Winkler RG, Nauss RE, Johs A, Parks JM, Yi Z, Cheng X, Liang L, Ohl M, Miller SM, Richter D, Gompper G, and Smith JC (2014).
Structure and Dynamics of a Compact State of a Multidomain Protein, the Mercuric Ion Reductase.
Biophysical Journal, 107(2):393-400.

Hong L, Smolin N, and Smith JC (2014).
de Gennes Narrowing Describes the Relative Motion of Protein Domains.
Physical Review Letters, 112:158102.

Johnson QR, Lindsay RJ, Raval SR, Dobbs JS, Nellas RB, and Shen T (2014).
Effects of Branched O-Glycosylation on a Semiflexible Peptide Linker.
The Journal of Physical Chemistry B, 118(8):2050-2057.

Langan P, Petridis L, O'Neill HM, Pingali SV, Foston M, Nishiyama Y, Schulz R, Lindner B, Hanson BL, Harton S, Heller WT, Urban V, Evans BR, Gnanakaran S, Ragauskas AJ, Smith JC, and Davison BH (2014).
Common Processes Drive the Thermochemical Pretreatment of Lignocellulosic Biomass.
Green Chemistry, 16:63-68.

Langan P, Sangha AK, Wymore T, Parks JM, Koo Yang Z, Leif Hanson B, Fisher Z, Mason SA, Blakeley MP, Trevor Forsyth V, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, and Kovalevsky A (2014).
L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study.
Structure, 22:1-14.

Le RK, Harris BJ, Iwuchukwu IJ, Bruce BD, Cheng X, Qian S, Heller WT, O'Neill H, and Frymier PD (2014).
Analysis of the Solution Structure of Thermosynechococcus elongatus Photosystem I in n-Dodecyl-β-D-Maltoside Using Small-Angle Neutron Scattering and Molecular Dynamics Simulation.
Archives of Biochemistry and Biophysics, 550:50-57.

Lian P, Guo H, Riccardi D, Dong A, Parks JM, Xu  Q, Pai EF, Miller SM, Wei DQ, Smith JC, and Guo H (2014).
X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs.
Biochemistry, 53(46):7211-7222.

Lin H, Hurt Jr. RA, Johs A, Parks JM, Morrell-Falvey JL, Liang L, Elias DA, and Gu B (2014).
Unexpected Effects of Gene Deletion on Interactions of Mercury with the Methylation-Deficient Mutant ΔhgcAB.
Environemntal Science &Technology Letters, 1(5):271-276.

Lopez-Garriga J, Wymore T, Pietri R, Roman-Morales EM, Rios-Gonzalez B, and Arbelo H (2014).
P90 Hydrogen Sulfide Activation by Hemeproteins: Implications of the Sulfheme Scenario.
Nitric Oxide, 39:S43.

Moritsugu K, Kidera A, and Smith JC (2014).
Solvent Friction Effects Propagate over the Entire Protein Molecule through Low-Frequency Collective Modes.
The Journal of Physical Chemistry B, 118(29):8559-8565.

Mostofian B, Cheng X, and Smith JC (2014).
Replica-Exchange Molecular Dynamics Simulations of Cellulose Solvated in Water and in the Ionic Liquid 1-Butyl-3-Methylimidazolium Chloride.
The Journal of Physical Chemistry B, 118(38):11037-11049.

Mostofian B, Smith JC, and Cheng X (2014).
Simulation of a Cellulose Fiber in Ionic Liquid Suggests a Synergistic Approach to Dissolution.
Cellulose, 21(2):983-997.

Pan J, Cheng X, Monticelli L, Heberle FA, Kucerka N, Tieleman DP, and Katsaras J (2014).
The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations.
Soft Matter, 10(21):3716-3725.

 
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