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2015

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

There are 39 references in this bibliography folder.

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Abraham MJ, Murtola T, Schulz R, Pall S, Smith JC, Hess B, and Lindahl E (2015).
GROMACS: High Performance Molecular Simulations through Multi-Level parallelism from Laptops to Supercomputers.
SoftwareX, 1-2:19-25.

Berthelier V, Harris JB, Estenson KN, and Baudry J (2015).
Discovery of an Inhibitor of Z-Alpha1 Antitrypsin Polymerization.
Plos One:e0126256.

Carmona C, Langan P, Smith JC, and Petridis L (2015).
Why Genetic Modification of Lignin Leads to Low-Recalcitrance Biomass.
Physical Chemistry Chemical Physics, 17:358-364.

Chen Q, Cheng X, Wei D, and Xu Q (2015).
Molecular Dynamics Simulation Studies of the Wild Type and E92Q/N155H Mutant of Elvitegravir-Resistance HIV-1 Integrase.
Interdisciplinary Sciences: Computational Life Sciences, 7(1):36-42.

Chen Q, Luan ZJ, Cheng X, and Xu JH (2015).
Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase.
Biochemistry, 54(9):1841-1848.

Chen Q, Luan ZJ, Yu HL, Cheng X, and Xu JH (2015).
Rational Design of a Carboxylic Esterase RhEst1 Based on Computational Analysis of Substrate Binding.
Journal of Molecular Graphics and Modelling, 62:319-324.

Chu Y, and Guo H (2015).
QM/MM MD and free energy simulation study of methyl transfer processes catalyzed by PKMTs and PRMTs.
Interdisciplinary Sciences: Computational Life Sciences:1-10.

Chu Y, and Guo H (2015).
QM/MM MD and Free Energy Simulation Study of Methyl Transfer Processes Catalyzed by PKMTs and PRMTs.
Interdisciplinary Sciences: Computational Life Sciences, 7(3):309-318.

Cournia Z, Allen T, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman T, Delemotte L, Del Val C, Freidman R, Gkeka P, Hege HC, Henin J, Kasimova M, Kolocouris A, Klein ML, Khalid S, Lemieu J, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, and Bondar AN (2015).
Membrane Proteins: Environmental Effects on Structure, Function and Dynamics.
Journal of Membrane Biology, 248(4):611-640.

Daidone I, Thukral L, Smith JC, and Amadei A (2015).
Monitoring the Folding Kinetics of a β-Hairpin by Time-Resolved IR Spectroscopy in Silico.
The Journal of Physical Chemistry B, 119(14):4849-4856.

Das A, Gerlits O, Parks J, Langan P, Kovalevsky A, and Heller W (2015).
Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation.
Structure, 23(12):2331-2340.

Ellingson SR, Miao Y, Baudry J, and Smith JC (2015).
Multi-Conformer Ensemble Docking to Difficult Protein Targets.
The Journal of Physical Chemistry B, 119(3):1026-1034.

Jiang Y, Chen H, Chen X, Köllner TG, Jia Q, Wymore TW, Wang F, and Chen F (2015).
Volatile Squalene from a Nonseed Plant Selaginella moellendorffii: Emission and Biosynthesis.
Plant Physiology and Biochemistry, 96:1-8.

Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, and Shen T (2015).
Mapping Allostery through Computational Glycine Scanning and Correlation Analysis of Residue–Residue Contacts.
Biochemistry, 54(7):1534-1541.

Johnson QR, Lindsay RJ, Petridis L, and Shen T (2015).
Investigation of Carbohydrate Recognition via Computer Simulation.
Molecules, 20(5):7700-7718.

Khadka NK, Cheng X, Ho CS, Katsaras J, and Pan J (2015).
Interactions of the Anticancer Drug Tamoxifen with Lipid Membranes.
Biophysical Journal, 108(10):2492-2501.

Lindner B, Petridis L, Langan P, and Smith JC (2015).
Determination of Cellulose Crystallinity from Powder Diffraction Patterns.
Biopolymers, 103(2):67-73.

Ming R, VanBuren R, Man Wai C, and al e (2015).
The pineapple genome and the evolution of CAM photosynthesis.
Nature Genetics, 47:1435-1442.

Mitchell JM, Clasman JR, June CM, Kaitany KCJ, LaFleur JR, Taracila MA, Klinger NV, Bonomo RA, Wymore T, Szareka A, Powers RA, and Leonard DA (2015).
Structural Basis of Activity against Aztreonam and Extended Spectrum Cephalosporins for Two Carbapenem-Hydrolyzing Class D β-Lactamases from Acinetobacter baumannii.
Biochemistry, 54(10):1976-1987.

Nickels J, Smith JC, and Cheng X (2015).
Lateral Organization, Bilayer Asymmetry, and Inter-Leaflet Coupling of Biological Membranes.
Chemistry and Physics of Lipids, 192:87-99.

Nickels JD, Cheng X, Mostofian B, Stanley C, Lindner B, Heberle FA, Perticaroli S, Feygenson M, Egami T, Standaert RF, Smith JC, Myles DAA, Ohl M, and Katsaras J (2015).
Mechanical Properties of Nanoscopic Lipid Domains.
2015, 137(50):15772–15780.

Pi M, Kapoor K, Wu Y, Ye R, Senogles SE, Nishimoto SK, Hwang DJ, Miller DD, Narayanan R, Smith JC, Baudry J, and Quarles LD (2015).
Structural and Functional Evidence for Testosterone Activation of GPRC6A in Peripheral Tissues.
Molecular Endocrinology, 29(12):1759-1773.

Qian P, Zhao N, Chen F, and Guo H (2015).
Understanding Substrate Specificity of Related Plant Methylesterases(MESs) from Computational Investigations.
Chemical Journal of Chinese Universities, 36(11):2283-2291.

Riccardi D, Parks JM, Johs A, and Smith JC (2015).
HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales.
Journal of Chemical Information and Modeling, 55(4):721-726.

 
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