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

There are 38 references in this bibliography folder.

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Cashman D, Ortega D, Zhulin I, and Baudry J (2013).
Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex.
PLoS ONE, 8(8):e70705.

Chaudret R, Parks JM, and Yang W (2013).
Pseudobond Parameters for QM/MM Studies Involving Nucleosides, Nucleotides, and Their Analogs.
The Journal of Chemical Physics, 138:045102.

Chen Q, Buolamwini JK, Smith JC, Li A, Xu Q, Cheng X, and Wei DQ (2013).
Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase.
Journal of Chemical Information and Modeling, 53(12):3297-3307.

Chu Y, Li G, and Guo H (2013).
QM/MM MD and Free Energy Simulations of the Methylation Reactions Catalyzed by Protein Arginine Methyltransferase PRMT3.
Canadian Journal of Chemistry, 91(7):605-612.

Davison BH, Parks JM, Davis MF, and Donohoe BS (2013).
Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion.
In: Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, ed. by C.E. Wyman. John Wiley & Sons, Ltd., chap. 3, pp. 23-35.

Devarajan A, Markutsya S, Lamm MH, Cheng X, Smith JC, Baluyut JY, Kholod Y, Gordon MS, and Windus TL (2013).
Ab initio Study of Molecular Interactions in Cellulose Iα.
The Journal of Physical Chemistry B, 117(36):10430-10443.

Ellingson SR, Smith JC, and Baudry J (2013).
VinaMPI: Facilitating Multiple Receptor High-Throughput Virtual Docking on High Performance Computers.
Journal of Computational Chemistry, 34(25):2212–2221.

GhattyVenkataKrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, and Cheng X (2013).
Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity.
Biophysical Journal, 104(4):904-912.

GhattyVenkataKrishna PK, Uberbacher EC, and Cheng X (2013).
Effect of the Amyloid β Hairpin’s Structure on the Handedness of Helices Formed by Its Aggregates.
FEBS Letters, 587(16):2649-2655.

Glass DC, Krishnan M, Smith JC, and Baudry J (2013).
Three Entropic Classes of Side Chains in a Globular Protein.
The Journal of Physical Chemistry B, 117(11):3127-3134.

Godec A, Smith JC, and Merzel F (2013).
Soft Collective Fluctuations Governing Hydrophobic Association.
Physical Review Letters, 111(12):127801.

Hong L, Glass DC, Nickels JD, Perticaroli S, Yi Z, Tyagi M, O'Neill H, Zhang Q, Sokolov AP, and Smith JC (2013).
Elastic and Conformational Softness of a Globular Protein.
Physical Review Letters, 110(2): 028104.

Jenkins D, Harris J, Howell E, Hinde R, and Baudry J (2013).
STAAR: Statistical analysis of aromatic rings.
Journal of Computational Chemistry, 34(6):518-522.

Lindner B, Petridis L, Schulz R, and Smith JC (2013).
Solvent-Driven Preferential Association of Lignin with Regions of Crystalline Cellulose in Molecular Dynamics Simulation.
Biomacromolecules, 14(10):3390-3398.

Lindner B, Yi Z, Prinz JH, Smith JC, and Noe F (2013).
Dynamic Neutron Scattering from Conformational Dynamics I: Theory and Markov Models.
The Journal of Chemical Physics, 139(17):175101.

Lu B, Cheng X, Huang J, and McCammon JA (2013).
AFMPB: An Adaptive Fast Multipole Poisson–Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems.
Computer Physics Communications, 184(11):2618-2619.

Mayes M, Jagadamma S, Ambaye H, Petridis L, and Lauter V (2013).
Neutron Reflectometry Reveals the Internal Structure of Natural Organic Matter Deposited onto an Aluminum Oxide.
Geoderma, 192:182-188.

McClintock C, Parks J, Bern M, GhattyVenkataKrishna P, and Hettich R (2013).
Comparative Informatics Analysis to Evaluate Site-Specific Protein Oxidation in Multidimensional LC–MS/MS Data.
Journal of Proteome Research, 12(7):3307-3316.

Miao Y, Hong L, Yi Z, and Smith JC (2013).
Zaccai Neutron Resilience and Site-Specific Hydration Dynamics in a Globular Protein.
The European Physical Journal E, 36:72.

Nellas R, Johnson Q, and Shen T (2013).
Solvent-Induced α- to 3_10-Helix Transition of an Amphiphilic Peptide.
Biochemistry, 52(40):7137–7144.

Ortega D, Mo G, Lee K, Zhou H, Baudry J, Dahlquist F, and Zhulin I (2013).
Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein.
PLoS Computational Biology, 9(11): e1003337.

Ortega D, Yang C, Ames P, Baudry J, Parkinson J, and Zhulin I (2013).
A Phenylalanine Rotameric Switch for Signal-State Control in Bacterial Chemoreceptors.
Nature Communications, 4:2881.

Parks JM, Johs A, Podar M, Bridou R, Hurt RA, Smith SD, Tomanicek SJ, Qian Y, Brown SD, Brandt CC, Palumbo AV, Smith JC, Wall JD, Elias DA, and Liang L (2013).
The Genetic Basis for Bacterial Mercury Methylation.
Science, 339(6125):1332-1335.

Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, and Lindahl E (2013).
GROMACS 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit. .
Bioinformatics, 29(7):845-854.

Qi X, Nellas R, Byrn M, Russell M, Bible A, Alexandre G, and Shen T (2013).
Swimming Motility Plays a Key Role in the Stochastic Dynamics of Cell Clumping.
Physical Biology, 10(2):026005.

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