Selected Publications


Mostofian, B et al.

Hu, X et al.

Nickels, J et al.

Wan, Q et al.

Ortega, D et al.

Parks, J et al.

Hong, L et al.

Brown, SD et al.

Petridis, L et al.

Journal Covers


Xiao, Z et al.

Vandavasi, VG et al.

Langan, P et al.

Yi, Z et al.

Miao, Y et al.

Zahran, M et al.

Kanzler, CR et al.



Parks JM, Johs A (2018)
Mercury methylation genes in bacteria and archaea
Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States)

Dajnowicz S, Parks JM, Hu X, Johnston RC, Kovalevsky AY, Mueser TC (2018)
Hyperconjugation promotes catalysis in a pyridoxal 5’-phosphate-dependent enzyme
ACS Catalysis, 8(7), 6733-6737

Cooper SJ, Krishnamoorthy G, Wolloscheck D, Walker JK, Rybenkov VV, Parks JM, Zgurskaya HI (2018)
Molecular Properties that Define the Activities of Antibiotics in Escherichia coli and Pseudomonas aeruginosa.
ACS infectious diseases, 4(8), 1223-1234

Lian P, Johnston RC, Parks JM, Smith JC (2018)
Quantum Chemical Calculation of pKas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines and Thiols in Aqueous Solution
The Journal of Physical Chemistry A, 122 (17), 4366-4374

Pavlova A, Parks JM, Gumbart JC (2018)
Development of CHARMM-compatible force-field parameters for cobalamin and related cofactors from quantum mechanical calculations
Journal of Chemical Theory and Computation, 14 (2), 784-798

Close D, Cooper S, Wang X, Giannone RJ, Engle NL, Tschaplinski TJ, Hedstrom L, Parks JM, Michener JK (2018)
Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis
bioRxiv, 315036

Langan PS, Vandavasi VG, Cooper SJ, Weiss KL, Ginell SL, Parks JM, Coates L (2018)
Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis
ACS Catal. 8 (3), 2428-2437

Goins CM, Dajnowicz S, Smith MD, Parks JM, Ronning DR (2018)
Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into Antigen 85 catalysis
Journal of Biological Chemistry, 293, 3651-3662

Kanzler CR, Lian P, Trainer EL, Yang X, Govind N, Parks JM, Graham AM (2018)
Emerging investigator series: Methylmercury speciation and dimethylmercury production in sulfidic solutions
Environmental Science: Processes & Impacts, 20 (4), 584-594

Smith JC, Tan P, Petridis L, Hong L (2018)
Dynamic Neutron Scattering by Biological Systems
Annual review of biophysics, 47, 335-354

Yang H, Watts HD, Gibilterra V, Weiss TB, Petridis L, Cosgrove DJ, Kubicki JD (2018)
Quantum Calculations on Plant Cell Wall Component Interactions
Interdisciplinary Sciences: Computational Life Sciences, 1-11

Vural D, Smith JC, Petridis L (2018)
Dynamics of the lignin glass transition
Physical Chemistry Chemical Physics, 20 (31), 20504-20512

Vural D, Gainaru C, O'Neill H, Pu Y, Smith MD, Parks JM, Pingali SV, Mamontov E, Davison BH, Sokolov AP, Ragauskas AJ, Smith JC, Petridis L (2018)
Impact of hydration and temperature history on the structure and dynamics of lignin
Green Chemistry, 20 (7), 1602-1611

Kumar R, Bhagia S, Smith MD, Petridis L, Ong RG, Cai CM, Mittal A, Himmel MH, Balan V, Dale BE, Ragauskas AJ, Smith JC, Wyman CE (2018)
Cellulose–hemicellulose interactions at elevated temperatures increase cellulose recalcitrance to biological conversion
Green Chemistry, 20 (4), 921-934

Moyer P, Smith MD, Abdoulmoumine N, Chmely SC, Smith JC, Petridis L, Labbé N (2018)
Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions
Physical Chemistry Chemical Physics, 20 (4), 2508-2516

Yang H, Wang T, Oehme D, Petridis L, Hong M, Kubicki JD (2018)
Structural factors affecting 13C NMR chemical shifts of cellulose: a computational study
Cellulose 25 (1), 23-36

Chirico G, Gansen A, Leuba SH, Olins AL, Olins DE, Smith JC, Tóth K (2018)
Jörg Langowski: his scientific legacy and the future it promises
BMC biophysics, 11 (1), 5

Vural D, Smith JC, Glyde HR (2018)
Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins
Biophysical journal, 114 (10), 2397-2407

Pi M, Kapoor K, Ye R, Hwang D, Miller DD, Smith JC, Baudry J, Quarles LD (2018)
Computationally identified novel agonists for GPRC6A
PloS one, 13 (4), e0195980

Pi M, Kapoor K, Ye R, Smith JC, Baudry J, Quarles LD (2018)
GPCR6A is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea
Molecular nutrition & food research, 62 (8), 1700770

Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC (2018)
Ensemble Docking in Drug Discovery
Biophysical journal, 114 (10), 2271-2278

Elghobashi-Meinhardt N, Phatak P, Bondar A, Elstner M, Smith JC (2018)
Catalysis of Ground State cis trans Isomerization of Bacteriorhodopsin’s Retinal Chromophore by a Hydrogen-Bond Network
The Journal of membrane biology, 1-13

Kovalevsky A, Aggarwal M, Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R (2018)
" To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation
Structure, 26 (3), 383-390. e3

Velazquez HA, Riccardi D, Xiao Z, Quarles LD, Yates CR, Baudry J, Smith JC (2018)
Ensemble docking to difficult targets in early‐stage drug discovery: Methodology and application to fibroblast growth factor 23
Chemical biology & drug design, 91 (2), 491-504

Xiao Z, Baudry J, Cao L, Huang J, Chen H, Yates CR, Li W, Dong B, Waters CM, Smith JC, Quarles LD (2018)
Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis
The Journal of clinical investigation, 128 (1), 157-174

Johnson QR, Mostofian B, Gomez GF, Smith JC, Cheng X (2018)
Effects of carotenoids on lipid bilayers
Physical Chemistry Chemical Physics, 20 (5), 3795-3804

Lindsay RJ, Pham B, Shen T, McCord RP (2018)
Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework
Nucleic Acids Research, 46 (16), 8143-8152

Lindsay RJ, Siess J, Lohry DP, McGee TS, Ritchie JS, Johnson QR, Shen T (2018)
T. Characterizing protein conformations by correlation analysis of coarse-grained contact matricesPhysical Chemistry Chemical
The Journal of Chemical Physics, 148 (2), 025101

Johnson QR, Lindsay RJ, Shen T  (2018)
CAMERRA: An Analysis Tool for the Computation of Allosteric Mechanism by Evaluating Residue-Residue Associations
Journal of Computational Chemistry, 39 (20), 1568-1578


Dajnowicz S, Johnston RC, Parks JM, Blakeley MP, Keen DA, Weiss KL, Gerlits O, Kovalevsky A, Mueser TC (2017)
Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme
Nature communications, 8 (1), 955

Zhou J, Smith MD, Cooper SJ, Cheng X, Smith JC, Parks JM (2017)
Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane
Environmental science & technology, 51 (18), 10595-10604

Haynes KM, Abdali N, Jhawar V, Zgurskaya HI, Parks JM, Green AT, Baudry J, Rybenkov VV, Smith JC, Walker JK (2017)
Identification and Structure–Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli
Journal of medicinal chemistry, 60 (14), 6205-6219

Pavlova A, Parks JM, Oyelere AK, Gumbart JC (2017)
Toward the rational design of macrolide antibiotics to combat resistance
Chemical Biology & Drug Design, 90 (5), 641-652

Goins CM, Dajnowicz S, Thanna S, Sucheck SJ, Parks JM, Ronning DR (2017)
Exploring covalent allosteric inhibition of antigen 85C from Mycobacterium tuberculosis by ebselen derivatives
ACS Infectious Diseases, 3 (5), 378-387

Dajnowicz S, Parks JM, Hu X, Gesler K, Kovalevsky AY, Mueser TC (2017)
Direct evidence that an extended hydrogen bonding network influences activation of pyridoxal 5′-phosphate in aspartate aminotransferase
Journal of Biological Chemistry, M116. 774588

Chen H, Johnston RC, Mann BF, Chu RK, Tolic N, Parks JM, Gu B (2017)
Identification of Mercury and Dissolved Organic Matter Complexes Using Ultrahigh Resolution Mass Spectrometry
Environmental Science & Technology Letters, 4 (2), 59-65

Vandavasi VG, Langan PS, Weiss KL, Parks JM, Cooper JB, Ginell SL, Coates L (2017)
Active-site protonation states in an acyl-enzyme intermediate of a class A β-lactamase with a monobactam substrate
Antimicrobial agents and chemotherapy, 61 (1), e01636-16

Abdali N, Parks JM, Haynes KM, Chaney JL, Green AT, Wolloscheck D, Walker JK, Rybenkov VV, Baudry J, Smith JC, Zgurskaya HI (2017)
Reviving antibiotics: efflux pump inhibitors that interact with AcrA, a membrane fusion protein of the AcrAB-TolC multidrug efflux pump
ACS Infectious Diseases, 3 (1), 89-98 

O’neill H, Pingali SV, Petridis L, He J, Mamontov E, Hong L, Urban V, Evans B, Langan P, Smith JC, Davison BH (2017)
Dynamics of water bound to crystalline cellulose
Scientific Reports, 7 (1), 11840

Polimeni M, Petridis L, Smith JC, Arcangeli C (2017)
Dynamics at a Peptide–TiO2 Anatase (101) Interface
The Journal of Physical Chemistry B, 121 (38), 8869-8877

Nickels JD, Chatterjee S, Mostofian B, Stanley CB, Ohl M, Zolnierczuk P, Schulz R, Myles DA, Standaert RF, Elkins JG, Cheng X, Katsaras J (2017)
Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane
The Journal of Physical Chemistry Letters, 8 (17), 4214-4217

Nickels JD, Chatterjee S, Stanley CB, Qian S, Cheng X, Myles DA, Standaert RF, Elkins JG, Katsaras J (2017)
The in vivo structure of biological membranes and evidence for lipid domains
PLoS biology, 15 (5), e2002214

Wall JS, Williams A, Stuckey A, Martin EB, Richey T, Wooliver C, Heidel RE, Cheng X, Kennel SJ (2017)
Probing the structural requirements of polybasic peptides for effective and specific amyloid reactivity
Amyloid, 24 (sup1), 30-31

Nickels JD, Chatterjee S, Stanley CB, Qian S, Cheng X, Myles DA, Standaert RF, Elkins JG, Katsaras J (2017)
Neutron scattering to study membrane systems: from lipid vesicles to living cells.
Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States)

Wall JS, Williams A, Martin EB, Cheng X, Kennel SJ (2017)
Serendipitous inhibition of Aβ and rVλ6Wil amyloid fibril growth by bi-functional peptides.
Amyloid, 24 (sup1), 32-33

Perticaroli S, Ehlers G, Stanley C, Mamontov E, O'Neill H, Zhang Q, Cheng X, Myles DA, Katsaras J, Nickels JD (2017)
Description of Hydration Water in Protein (GFP) Solution
Biophysical Journal, 112 (3), 201a

Nickels JD, Chatterjee S, Stanley C, Qian S, Cheng X, Myles DA, Standaert R, Elkins J, Katsaras J (2017)
Neutron Scattering to Study Membrane Systems: From Model Membranes to Living Cells
Biophysical Journal, 112 (3), 224a

Vural D, Hu X, Lindner B, Jain N, Miao Y, Cheng X, Liu Z, Hong L, Smith JC (2017)
Quasielastic neutron scattering in biology: theory and applications
Biochimica et Biophysica Acta (BBA)-General Subjects, 1861 (1), 3638-3650

Perticaroli S, Mostofian B, Ehlers G, Neuefeind JC, Diallo SO, Stanley CB, Daemen L, Egami T, Katsaras J, Cheng X, Nickels JD (2017)
Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid
Physical Chemistry Chemical Physics, 19 (38), 25859-25869

He H, Weir RL, Toutounchian JJ, Pagadala J, Steinle JJ, Baudry J, Miller DD, Yates CR (2017)
The quinic acid derivative KZ-41 prevents glucose-induced caspase-3 activation in retinal endothelial cells through an IGF-1 receptor dependent mechanism
PloS one 12 (8), e0180808

Jing X, Falcon WE, Baudry J, Serpersu EH (2017)
Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability: Can We Draw a Line?
The Journal of Physical Chemistry B 121 (29), 7086-7094

Dale JB, Smeesters PR, Courtney HS, Penfound TA, Hohn CM, Smith JC, Baudry JY (2017)
Structure-based design of broadly protective group a streptococcal M protein-based vaccines
Vaccine 35 (1), 19-26

Chowdhary J, Loeffler FF, and Smith JC (2017).
Community detection in sequence similarity networks based on attribute clustering.
PLOSone, 12(7):E0178650.

Cortini R, Cheng X, Smith JC, and Kornyshev AA (2017).
The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations.
Journal of Physics: Condensed Matter, 29(8).

Dale JB, Smeesters PR, Courtney HS, Penfound TA, Hohn CM, and Smith JC (2017).
Structure-based design of broadly protective group a streptococcal M protein-based vaccines.
Vaccine, 35(1):19-26.

Liu Z, Huang J, Tyagi M, O'Neill H, Zhang Q, Mamontov E, Jain N, Wang Y, Zhang J, Smith JC, and Hong L (2017).
Dynamical Transition of Collective Motions in Dry Proteins.
Physical Review Letters, 119(4):48101.

Simakov N, Leonard DA, Smith JC, Wymore T, and Szarecka A (2017).
A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop.
The Journal of Physical Chemistry B, 121(15):3285-3296.

Smith JC (2017).
Pickin' up Good Vibrations.
Biophysical Journal, 112(5):829-830.

Toutounchian JJ, Pagadala J, Miller DD, Baudry J, Park F, Chaum E, and Yates CR (2017).
Novel Small Molecule JP-153 Targets the Src-FAK-Paxillin Signaling Complex to Inhibit VEGF-Induced Retinal Angiogenesis.
Molecular Pharmacology, 91(1).

Xiao Z, Riccardi D, Velazquez HA, Chin AL, Yates CR, Carrick JD, Baudry J, Smith JC, and Quarles LD (2017).
A Computationally Identified Compound Antagonizes Excess FGF-23 Signaling in Renal Tubules and a Mouse Model of Hypophosphatemia.
Science Signaling, 9(455):ra113.

Bondar, AN, Smith JC (2017).
Protonation–state‐Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins
Photochemistry and photobiology, 93 (6), 1336-1344


Aggarwal M, Kovalevsky A, Velazquez H, Zoeuml S, Smith J, and McKenna R (2016).
Neutron Structure of Human Carbonic Anhydrase II in Complex with Methazolamide: Mapping the Solvent and H-Bonding Patterns of an Effective Clinical Drug.
IUCrJ, 3(5):319-325.

Arbelo-Lopez HD, Simakov NA, Smith JC, Lopez-Garriga J, and Wymore T (2016).
Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme.
The Journal of Physical Chemistry B, 120(30):7319-7331.

Clark AK, Wilder JH, Grayson AW, Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, and Shen T (2016).
The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor.
The Journal of Physical Chemistry B.

Das A, Gerlits O, Parks JM, Langan P, Kovalevsky A, and Heller WT (2016).
Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation.
Structure, 23(12):2331-2340.

Evangelista W, Weir RL, Ellingson SR, Harris JB, Kapoor K, Smith JC, and Baudry J (2016).
Ensemble-based docking: From hit discovery to metabolism and toxicity predictions.
Bioorganic & Medicinal Chemistry, 24(20):4928-4935.

Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, and Kovalevsky A (2016).
Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.
Angewandte Chemie, 128(16):5008-5011.

Harris BJ, Cheng X, and Frymier P (2016).
Structure and Function of Photosystem I–[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study.
The Journal of Physical Chemistry B, 120(4):599-609.

Hong L, Jain N, Cheng X, Bernal A, Tyagi M, and Smith JC (2016).
Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering.
Science Advances, 2(10).

Hu X, Hong L, Smith MD, Neusius T, Cheng X, and Smith JC (2016).
The Dynamics of Single Protein Molecules is Non-Equilibrium and Self-Similar over Thirteen Decades in Time.
Nature Physics, 12:171-174.

Johnson QR, Lindsay RJ, Nellas RB, and Shen T (2016).
Pressure-induced conformational switch of an interfacial protein.
Proteins: Structure, Function, and Bioinformatics, 84(6):820-827.

Johnston RC, Zhou J, Smith JC, and Parks JM (2016).
Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin.
The Journal of Physical Chemistry B, 120(30):7307-7318.

Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, and Baudry J (2016).
Highly Dynamic Anion–Quadrupole Networks in Proteins.
Biochemistry, 55(43):6056-6069.

Kapoor K, McGill N, Paterson CB, Meyers HV, Blackburn MN, and Baudry J (2016).
Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex.
The Journal of Chemical Information and Modeling, 56(3):535-547.

Kapoor K, McGill N, Peterson CB, Meyers HV, Blackburn MN, and Baudry J (2016).
Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex.
Journal of Chemical Information and Modeling, 56(3):535-547.

Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, and Shen T (2016).
DMSO enhanced conformational switch of an interfacial enzyme.
Biopolymers, 105(12).

Lv C, Aitchison EW, Wu D, Zheng L, Cheng X, and Yang W (2016).
Comparative Exploration of Hydrogen Sulfide and Water Transmembrane Free Energy Surfaces via Orthogonal Space Tempering Free Energy Sampling.
Journal of Computational Chemistry, 37(6):567-574.

Lv C, Aitchison EW, Wu D, Zheng L, Cheng X, and Yang W (2016).
Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling.
Journal of Computational Chemistry, 37(6):567-574.

Miao Y, Baudry J, Smith JC, and McCammon JA (2016).
General Trends of Dihedral Conformational Transitions in a Globular Protein.
Proteins: Structure, Function, and Bioinformatics, 84(4):501-514.

Mostofian B, Cai C, Smith M, Petridis L, Cheng X, Wyman C, and Smith J (2016).
Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications.
Journal of the American Chemical Society, 138(34):10869-10878.

Pi M, Kapoor K, Ye R, Nishimoto SK, Smith JC, Baudry J, and Quarles LD (2016).
Evidence for Osteocalcin Binding and Activation of GPRC6A in β-Cells.
Endocrinology, 157(5):1866-1880.

Sangha AK, Petridis L, Cheng X, and Smith JC (2016).
Relative Binding Affinities of Monolignols to Horseradish Peroxidase.
The Journal of Physical Chemistry B, 120(31):7635-7640.

Smith M, Mostofian B, Cheng X, Petridis L, Cai C, Wyman C, and Smith J (2016).
Cosolvent Pretreatment in Cellulosic Biofuel Production: Effect of Tetrahydrofuran-Water on Lignin Structure and Dynamics.
Green Chemistry, 18(5):1268-1277.

Smith MD, Mostofian B, Petridis L, Cheng X, and Smith JC (2016).
Molecular Driving Forces Behind the Tetrahydrofuran-Water Miscibility Gap.
The Journal of Physical Chemistry B, 120(4):740-747.

Smith MD, Petridis L, Cheng X, Mostofian B, and Smith JC (2016).
Enhanced Sampling Simulation Analysis of the Structure of Lignin in the THF-Water Miscibility Gap.
Physical Chemistry Chemistry Physics, 18(9):6394-6398.

Trizac E, and Shen T (2016).
Bending stiff charged polymers: The electrostatic persistence length.
Europhysics Letters (EPL), 116(1).

Vandavasi V, Putnam DK, Zhang Q, Petridis L, Heller WT, Nixon BT, Haigler CH, Kalluri U, Coates L, Langan P, Smith JC, Meiler J, and O'Neill H (2016).
A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers.
Plant Physiology, 170(1):123-135.

Walden DM, Ogba OM, Johnston RC, and Cheong PHY (2016).
Computational Insights into the Central Role of Nonbonding Interactions in Modern Covalent Organocatalysis.
Accounts of Chemical Research, 49(6):1279-1291.

Xiao Z, Riccardi D, Velazquez H, Chin A, Yates C, Carrick J, Smith J, Baudry J, and Quarles L (2016).
A Computationally Identified Compound Antagonizes Excess FGF-23 Signaling in Renal Tubules and a Mouse Model of Hypophosphatemia.
Science Signaling, 9(455):ra113.

Zhao N, Lin H, Lan S, Jia Q, Chen X, Guo H, and Chen F (2016).
VvMJE1 of the grapevine (Vitis vinifera) VvMES methylesterase family encodes for methyl jasmonate esterase and has a role in stress response.
Plant Physiology and Biochemistry, 102:125-132.

Zheng K, Wang X, Weighill DA, Gue HB, Xie M, Yang Y, Yang J, Wang S, Jacobson DA, Guo H, Muchero W, Tuskan GA, and Chen JG (2016).
Characterization of DWARF14 Genes in Populus.
Scientific Reports, 6(21593).


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.

Shen T, and Wong CF (2015).
Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program.
In: Computational Peptidology, ed. by Peng Zhou, Jian Huang. Springer, New York, vol. 1268, chap. 5, pp. 75-87. Methods in Molecular Biology. (ISBN: 978-1-4939-2285-7).

Smith S, Bridou R, Johs A, Parks J, Elias D, Hurt. Jr. R, Brown S, Podar M, and Wall J (2015).
Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation.
Applied and Environmental Microbiology, 81(9):3205-3217.

Smith SD, Bridou R, Johs A, Parks JM, Elias DA, Hurt Jr RA, Brown SD, Podar M, and Wall JD (2015).
Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation.
Applied and Environmental Microbiology, 81(9):3205-3217.

Vermaas JV, Petridis L, Qi X, Schulz R, Lindner B, and Smith JC (2015).
Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction.
Biotechnology for Biofuels, 8:217.

Vural D, Hong L, Smith JC, and Glyde H (2015).
Motional Displacements in Proteins: The Origin of Wave-Vector-Dependent Values.
Physical Review E, 91:052705.

Wall JS, Martin EB, Richey T, Stuckey AC, Macy S, Wooliver C, Williams A, Foster JS, McWilliams-Koeppen P, Ubebacher E, Cheng X, and Kennel SJ (2015).
Preclinical Validation of the Heparin-Reactive Peptide p5+14 as a Molecular Imaging Agent for Visceral Amyloidosis.
Molecules, 20(5):7657-7682.

Wan Q, Parks J, Hanson BL, Fisher S, Ostermann A, Schrader T, Graham D, Coates L, Langan P, and Kovalevsky A (2015).
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
Proceedings of the National Academy of Sciences of the United States of America, 112(40):12384-12389.

Wan Q, Parks J, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L,
Direct Determination of Protonation States and Visualization of Hydrogen Bonding in a Glycoside Hydrolase with Neutron Crystallography.
Proceedings of the National Academy of Sciences of the United States of America, 112(40):12384–12389.

Wolter T, Elstner M, Fischer S, Smith JC, and Bondar AN (2015).
Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States.
The Journal of Physical Chemistry B, 119(6):2229-2240.

Yao J, Guo H, and Yang X (2015).
PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction.
International Journal of Genomics, 2015:608042.


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.

Petridis L, O'Neill H, Johnsen M, Fan B, Schulz R, Mamontov E, Maranas J, Langan P, and Smith J (2014).
Hydration Control of the Mechanical and Dynamical Properties of Cellulose.
Biomacromolecules, 15(11):4152-4159.

Pingali SV, O'Neill HM, Nishiyama Y, He L, Melnichenko YB, Urban V, Petridis L, Davison B, and Langan P (2014).
Morphological Changes in the Cellulose and Lignin Components of Biomass Occur at Different Stages during Steam Pretreatment.
Cellulose, 21(2):873-878.

Rajeshwar T. R, Smith JC, and Krishnan M (2014).
Hidden Regularity and Universal Classification of Fast Side Chain Motions in Proteins.
Journal of the American Chemical Society, 136(24):8590-8605.

Sangha AK, Davison BH, Standaert RF, Davis MF, Smith JC, and Parks JM (2014).
Chemical Factors that Control Lignin Polymerization.
The Journal of Physical Chemistry B, 118(1):164-170.

Srinivas G, Cheng X, and Smith JC (2014).
Coarse-Grain Model for Natural Cellulose Fibrils in Explicit Water.
The Journal of Physical Chemistry B, 118(11):3026-3034.

Wymore T, Field MJ, Langan P, Smith JC, and Parks JM (2014).
Hydrolysis of DFP and the Nerve Agent (S)-Sarin by DFPase Proceeds along Two Different Reaction Pathways: Implications for Engineering Bioscavengers.
The Journal of Physical Chemistry B, 118(17):4479-4489.

Zhou J, Riccardi D, Beste A, Smith JC, and Parks JM (2014).
Mercury methylation by HgcA: Theory supports carbanion transfer to Hg(II).
Inorganic Chemistry, 53(2):772-777.


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.

Riccardi D, Guo HB, Parks JM, Gu B, Liang L, and Smith JC (2013).
Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations.
Journal of Chemical Theory and Computation, 9(1):555-569.

Riccardi D, Guo HB, Parks JM, Gu B, Summers AO, Miller SM, Liang L, and Smith JC (2013).
Why Mercury Prefers Soft Ligands.
The Journal of Physical Chemistry Letters, 4(14): 2317-2322.

Sawada D, Nishiyama Y, Petridis L, Parthasarathi R, Gnanakaran S, Forsyth VT, Wada M, and Langan P (2013).
Structure and Dynamics of a Complex of Cellulose with EDA: Insights into the Action of Amines on Cellulose.
Cellulose, 20(4):1563-1571.

Sharma H, Sanchez TW, Neamati N, Detorio M, Schinazi RF, Cheng X, and Buolamwini JK (2013).
Synthesis, Docking, and Biological Studies of Phenanthrene β-Diketo Acids as Novel HIV-1 Integrase Inhibitors.
Bioorganic & Medicinal Chemistry Letters, 23(22):6146–6151.

Shen T, Qi X, and Nellas R (2013).
Nucleation Dynamics of Active Particles.
The Journal of Physical Chemistry B, 117(42):12844–12849.

Smith JC, and Roux B (2013).
Eppur Si Muove! The 2013 Nobel Prize in Chemistry.
Structure, 21(12):2102-2105.

Vural D, Hong L, Smith JC, and Glyde H (2013).
Long-Time Mean Square Displacements in Proteins.
Physical Review E, 88:052706 .

Wang X, Yang T, Cheng X, and Shen Q (2013).
Enantioselective Electrophilic Trifluoromethylthiolation of β-Ketoesters: A Case of Reactivity and Selectivity Bias for Organocatalysis.
Angewandte Chemie International Edition, 52(49):12860-12864.

Yi Z, Lindner B, Prinz JH, Noe F, and Smith J (2013).
Dynamic Neutron Scattering from Conformational Dynamics. II. Application Using Molecular Dynamics Simulation and Markov Modeling.
The Journal of Chemical Physics, 139(17):175102.

Zhang B, Lu B, Cheng X, Huang J, Pitsianis N, Sun X, and McCammon A (2013).
Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver.
Communications in Computational Physics, 13(1):107-128.

Zhao N, Yao J, Chaipransongsuk M, Li G, Guan J, Tschaplinski TJ, Guo H, and Chen F (2013).
Molecular and Biochemical Characterization of the Jasmonic Acid Methyltransferase Gene from Black Cottonwood (Populus trichocarpa).
Phytochemistry, 94:74-81.


Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, and Gnanakaran S (2012).
A Coarse-Grained Model for Synergistic Action of Multiple Enzymes on Cellulose.
Biotechnology for Biofuels, 5(1):55.

Berezniak T, Jaeschke A, Smith JC, and Imhof P (2012).
Stereoselection in the Diels-Alderase Ribozyme: A Molecular Dynamics Study.
Journal of Computational Chemistry, 33(19):1603-1614.

Biswas M, Wocjan T, Langowski J, and Smith JC (2012).
DNA Bending Potentials for Loop-Mediated Nucleosome Repositioning .
Europhysics Letters, 97(3):38004.

Brothers MC, Nesbitt AE, Hallock MJ, Rupasinghe SG, Tang M, Harris J, Baudry J, Schuler MA, and Rienstra CM (2012).
VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy.
Journal of Biomolecular NMR, 52(1):41-56.

Cheng X, and Ivanov I (2012).
Molecular Dynamics.
Methods in Molecular Biology, 929:243-285.

Cheng X, Parks JM, Petridis L, Lindner B, Schulz R, Guo HB, Srinivas G, and Smith JC (2012).
Molecular Simulation in the Energy Biosciences.
In: Innovations in Biomolecular Modeling and Simulations, ed. by T. Schlick. RSC Publishing, chap. 5, pp. 87-114. (ISBN: 978-1-84973-504-9 ).

Daidone I, Iacobucci C, McLain SE, and Smith JC (2012).
Alteration of Water Structure by Peptide Clusters Revealed by Neutron Scattering in the Small-Angle Region (below 1 Å^−1).
Biophysical Journal, 103(7):1518-1524.

Glass DC, Moritsugu K, Cheng X, and Smith JC (2012).
REACH Coarse-Grained Simulation of a Cellulose Fiber.
Biomacromolecules, 13(9):2634–2644.

Guo HB, He F, Gu B, Liang L, and Smith JC (2012).
Time-Dependent Density Functional Theory Assessment of UV Absorption of Benzoic Acid Derivatives.
The Journal of Physical Chemistry A, 116(48):11870–11879.

Hong L, Glass DC, and Smith JC (2012).
Surface Hydration Amplifies Single-Well Protein Atom Diffusion Propagating into the Macromolecular Core.
Physical Review Letters, 108(23):238102.

Johnson QR, Nellas RB, and Shen T (2012).
Solvent-Dependent Gating Motions of an Extremophilic Lipase from Pseudomonas aeruginosa.
Biochemistry, 51(31):6238-6245.

Krishnan M, and Smith JC (2012).
Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters.
The Journal of Physical Chemistry B, 116(14):4124-4133.

Langan P, Evans BR, Foston M, Heller WT, O'Neill H, Petridis L, Pingali SV, Ragauskas AJ, Smith JC, Urban VS, and Davison BH (2012).
Neutron Technologies for Bioenergy Research.
Industrial Biotechnology, 8(4):209-216.

Lindner B, and Smith JC (2012).
Sassena - X-ray and Neutron Scattering Calculations from Molecular Dynamics Trajectories using Massively Parallel Computers.
Computer Physics Communications, 183(7):1491-1501.

Merzel F, Johnson MR, and Smith JC (2012).
Normal Modes and Neutrons: Defining Collective, Functional Biomolecular Motions.
Neutron News, 3(23):26-30.

Miao Y, Yi Z, Cantrell C, Glass DC, Baudry J, and Smith JC (2012).
Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR and Molecular Dynamics Simulation.
Biophysical Journal, 103(10):2167-2176.

Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, and Smith JC (2012).
Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein.
Journal of the American Chemical Society, 134(48):19576-19579.

Mintz BJ, and Parks JM (2012).
Benchmark Interaction Energies for Biologically Relevant Noncovalent Complexes Containing Divalent Sulfur.
The Journal of Physical Chemistry A, 116(3):1086-1092.

Nellas RB, Glover MM, Hamelberg D, and Shen T (2012).
High-Pressure Effect on the Dynamics of Solvated Peptides.
The Journal of Chemical Physics, 136:145103.

Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, and Sokolov AP (2012).
Dynamics of a Protein and Its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP.
Biophysical Journal, 104(7):1566-1575.

Pan J, Cheng X, Heberle FA, Mostofian B, Kucerka N, Drazba P, and Katsaras J (2012).
Interactions between Ether Phospholipids and Cholesterol As Determined by Scattering and Molecular Dynamics Simulations.
The Journal of Physical Chemistry B, 116(51):14829-14838.

Pool R, Heringa J, Hoefling M, Schulz R, and Smith JC (2012).
Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of GROMACS through the GromPy Python Interface Module to the GROMACS Simulation C-library.
Journal of Computational Chemistry, 33(12):1207-1214.

Sangha A, Petridis L, Smith JC, Ziebell A, and Parks JM (2012).
Molecular Simulation as a Tool for Studying Lignin.
Environmental Progress & Sustainable Energy, 31(1):47-54.

Sangha AK, Parks JM, Standaert RF, Ziebell A, Davis M, and Smith JC (2012).
Radical Coupling Reactions in Lignin Synthesis: A Density Functtional Theory Study.
The Journal of Physical Chemistry B, 116(16):4760-4768.

Sharma H, Cheng X, and Buolamwini JK (2012).
Homology Model-Guided 3D-QSAR Studies of HIV-1 Integrase Inhibitors.
Journal of Chemical Information and Modeling, 52(2):515-544.

Tschaplinski TJ, Standaert RF, Engle NL, Martin MZ, Sangha AK, Parks JM, Smith JC, Samuel R, Pu Y, Ragauskas AJ, Hamilton CY, Fu C, Wang ZY, Davison BH, Dixon RA, and Mielenz JR (2012).
Down-Regulation of the Caffeic Acid O-Methyltransferase Gene in Switchgrass Reveals a Novel Monolignol Analog.
Biotechnology for Biofuels, 5:71.

Ulmschneider JP, Smith JC, Ulmschneider MB, Ulrich AS, and Strandberg E (2012).
Reorientation and Dimerization of the Membrane-Bound Antimicrobial PeptidePGLa from Microsecond All-Atom MD Simulations.
Biophysical Journal, 103(3):472-482.

Voltz K, Trylska J, Calimet N, Smith JC, and Langowski J (2012).
Unwrapping of Nucleosomal DNA Ends: A Multiscale Molecular Dynamics Study.
Biophysical Journal, 102(4):849-858.

Wang HL, Cheng X, and Sine SM (2012).
Intramembrane Proton Binding Site Linked to Activation of Bacterial Pentameric Ion Channel.
The Journal of Biological Chemistry, 287(9):6482-6489.

Ye X, Yuan S, Guo H, Chen F, Tuskan GA, and Cheng ZM (2012).
Evolution and Divergence in the Coding and Promoter Regions of the Populus Gene Family Encoding Xyloglucan Endotransglycosylase/Hydrolases.
Tree Genetics & Genomes, 8(1):177-194.

Yi Z, Miao Y, Baudry J, Jain N, and Smith JC (2012).
Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering.
The Journal of Physical Chemistry B, 116(16):5028-5036.


Balog E, Perahia D, Smith JC, and Merzel F (2011).
Vibrational Softening of a Protein on Ligand Binding.
The Journal of Physical Chemistry B, 115(21):6811-6817.

Biswas M, Voltz K, Smith JC, and Langowski J (2011).
Role of Histone Tails in Structural Stability of the Nucleosome.
PLoS Computational Biology, 7(12): e1002279.

Bondar AN, Fischer S, and Smith JC (2011).
Water Pathways in the Bacteriorhodopsin Proton Pump .
Journal of Membrane Biology, 239(1-2):73-84.

Bondar AN, Knapp-Mohammady M, Suhai S, Fischer S, and Smith JC (2011).
Ground-State Properties of the Retinal Molecule: from Quantum Mechanical to Classical Mechanical Computations of Retinal Proteins.
Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 130(4-6):1169-1183.

Brown SD, Guss AM, Karpinets TV, Parks JM, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwand A, Rodriguez M, Raman B, Shao X, Mielenz JR, Smith JC, Keller M, and Lynd LR (2011).
Mutant Alcohol Dehydrogenase Leads to Improved Ethanol Tolerance in Clostridium thermocellum.
Proceedings of the National Academy of Sciences (U.S.A.), 108(33):13752-13757.

Collignon B, Schulz R, Smith JC, and Baudry J (2011).
Task-Parallel MPI Implementation of Autodock4 for Docking of Very Large Databases of Compounds Using High Performance Super-Computers.
Journal of Computational Chemistry, 32(6):1202-1209.

Daidone I, Di Nola A, and Smith JC (2011).
Molecular Origin of Gerstmann-Sträussler-Scheinker Syndrome: Insight from Computer Simulation of an Amyloidogenic Prion Peptide.
Biophysical Journal, 100(12):3000-3007.

Ellingson SR, and Baudry J (2011).
High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud.
In: Proceedings of the second international workshop on Emerging computational methods for the life sciences, ed. by ECMLS '11. ACM, chap. 5, pp. 33-38. (ISBN: 978-1-4503-0702-4).

Fritsch S, Ivanov I, Wang H, and Cheng X (2011).
Ion Selectivity Mechanism in a Bacterial Pentameric Ligand-Gated Ion Channel.
Biophysical Journal, 100(2):390-398.

Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Andrew Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, and Korber B (2011).
Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections.
PLOS Pathogens, 7(9): e1002209.

Godec A, Smith JC, and Merzel F (2011).
Increase of both Order and Disorder in the First Hydration Shell with Increasing Solute Polarity.
Physical Review Letters, 107(26):267801.

Guo HB, Parks JM, Johs A, and Smith JC (2011).
Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage.
In: Modeling of Molecular Properties, ed. by Peter Comba. Wiley, chap. 20, pp. 311-324.

Hembree W, and Baudry J (2011).
Three-dimensional Mapping of Micro-environmental Control of Methyl Rotational Barriers.
Journal of Physical Chemistry B, 115(26):8575-8580.

Hong L, Lindner B, Smolin N, Sokolov A, and Smith JC (2011).
Three Classes of Motion in the Dynamic Neutron-Scattering Susceptibility of a Globular Protein.
Physical Review Letters, 107(14):148102.

Hu X, Elghobashi-Meinhardt N, Gembris D, and Smith JC (2011).
Response of Water to Electric Fields at Temperatures Below the Glass Transition: A Molecular Dynamics Analysis.
Journal of Chemical Physics, 135:134507.

Hu X, Norris A, Baudry J, and Serpersu E (2011).
Coenzyme A Binding to the Aminoglycoside Acetyltransferase (3)-IIIb Increases Conformational Sampling of Antibiotic Binding Site.
Biochemistry, 50(48):10559-10565.

Johs A, Harwood IM, Parks JM, Nauss RE, Smith JC, Liang L, and Miller SM (2011).
Structural Characterization of Intramolecular Hg2+ Transfer between Flexibly Linked Domains of Mercuric Ion Reductase.
Journal of Molecular Biology, 413 (3):639–656.

Klein H, Cheng X, Smith JC, and Shen T (2011).
Transfer Matrix Approach to the Hydrogen-Bonding in Cellulose Ia Fibrils Describes the Recalcitrance to Thermal Deconstruction.
Journal of Physical Chemistry, 135(8):085106.

Li L, Jiang X, Guan H, Wang P, and Guo H (2011).
Three Alginate Lyases from Marine Bacterium Pseudomonas fluorescens HZJ216: Purification and Characterization.
Applied Biochemistry and Biotechnology, 164(3):305-317.

Miao Y, and Baudry J (2011).
Active Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process.
Biophysical Journal, 101(6):1493-1503.

Mostofian B, Smith JC, and Cheng X (2011).
The Solvation Structures of Cellulose Microfibrils in Ionic Liquids.
Interdisciplinary Sciences - Computational Life Sciences, 3(4):308-320.

Neusius T, Daidone I, Sokolov I, and Smith JC (2011).
Configurational Subdiffusion of Peptides: A Network Study.
Physical Review E, 83:021902.

Noe F, Doose S, Daidone I, Lollmann M, Sauer M, Chodera JD, and Smith JC (2011).
Dynamical Fingerprints: Probing Individual Relaxation Processes in Biomolecular Dynamics with Simulations and Kinetic Experiments.
Proceedings of the National Academy of Sciences (U.S.A), 108(12):4822-4827.

Petridis L, Pingali SV, Urban V, Heller W, O' Neil H, Foston M, Ragauskas A, and Smith JC (2011).
Self-Similar Multiscale Structure of Lignin Revealed by Neutron Scattering and Molecular Dynamics Simulation.
Physical Review E, 83:061911.

Petridis L, Schulz R, and Smith JC (2011).
Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics.
Journal of the American Chemical Society, 133(50):20277–20287.

Petridis L, Xu J, Crowley M, Smith JC, and Cheng X (2011).
Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes.
In: Computational Modeling in Lignocellulosic Biofuel Production, ed. by M. R. Nimlos and M. F. Crowley. ACS Publications, vol. 1052, chap. 3, pp. 55-73. (ISBN: 9780841225718).

Philip V, Harris J, Adams R, Nguyen D, Spiers J, Baudry J, Howell E, and Hinde R (2011).
A Survey of Aspartate−Phenylalanine and Glutamate−Phenylalanine Interactions in the Protein Data Bank: Searching for Anion−π Pairs.
Biochemistry, 50(14):2939-2950.

Pingali SV, O'Neill HM, McGaughey J, Urban VS, Rempe CS, Petridis L, Smith JC, Evans BR, and Heller WT (2011).
Small-Angle Neutron Scattering Reveals pH-Dependent Conformational Changes in Trichoderma reesei Cellobiohydrolase I: Implications for Enzymatic Activity.
Journal of Biological Chemistry, 286:32801-32809.

Prinz JH, Chodera J, Pande V, Swope W, Smith JC, and Noe F (2011).
Optimal Use of Data in Parallel Tempering Simulations for the Construction of Discrete-State Markov Models of Biomolecular Dynamics.
Journal of Chemical Physics, 134:244108.

Prinz JH, Held M, Smith JC, and Noe F (2011).
Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes.
Multiscale Modeling and Simulation, 9(2):545-567.

Saharay M, Guo HB, Smith JC, and Guo H (2011).
QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates.
In: Computational Modeling in Lignocellulosic Biofuel Production, ed. by M. R. Nimlos and M. F. Crowley. ACS Publications, vol. 1052, chap. 7, pp. 135-154. (ISBN: 9780841225718).

Smith JC, Krishnan M, Smolin N, and Petridis L (2011).
Integration of Neutron Scattering with Computer Simulation to Study the Structure and Dynamics of Biological Systems.
In: Dynamics of Biological Macromolecules by Neutron Scattering, ed. by S. Magazu. Bentham Science Publishers, chap. IV, pp. 99-108. (ISBN: 978-1-60805-219-6 ).

Splettstoesser T, Holmes KC, Noe F, and Smith JC (2011).
Structural Modeling and Molecular Dynamics Simulation of the Actin Filament.
PROTEINS: Structure, Function, and Bioinformatics, 79(7):2033-2043.

Srinivas G, Cheng X, and Smith JC (2011).
A Solvent-Free Coarse-Grain Model for Crystalline and Amorphous Cellulose Fibrils.
Journal of Chemical Theory and Computation, 7(8):2539–2548.

Thukral L, Daidone I, and Smith JC (2011).
Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations.
PLos Computational Biology, 7(9): e1002137.

Ulmschneider JP, Smith JC, White S, and Ulmschneider MB (2011).
In Silico Partitioning and Transmembrane Insertion of Hydrophobic Peptides Under Equilibrium Conditions.
Journal of the American Chemical Society, 133(39):15487–15495.

Wang S, Shen T, and Wolynes P (2011).
The Interplay of Nonlinearity and Architecture in Equilibrium Cytoskeletal Mechanics.
Journal of Chemical Physics, 134(1):014510.

Xu Z, Cai W, and Cheng X (2011).
Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model.
Communication in Computational Physics, 9(4):1056-1070.

Xu Z, Cheng X, and Yang H (2011).
Treecode-Based Generalized Born Method.
Journal of Chemical Physics, 134(6):064107.

Yao J, Nellas R, Glover M, and Shen T (2011).
Stability and Sugar Recognition Ability of Ricin-Like Carbohydrate Binding Domains.
Biochemistry, 50(19):4097–4104.

Yao J, Xu Q, Chen F, and Guo H (2011).
QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity.
The Journal of Physical Chemistry B, 115(2):389-396.

Zahran M, Berezniak T, Imhof P, and Smith JC (2011).
Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease.
FEBS Letters, 585(17):2739-2743.


Bellesia G, Asztalos A, Shen T, Langan P, Redondo A, and Gnanakaran S (2010).
In Silico Studies of Crystalline Cellulose and Its Degradation by Enzymes.
ACTA Crystallographica. Section D: Biological Crystallography , 66(11):1184-1188.

Berezniak T, Zahran M, Imhof P, Jaeschke A, and Smith JC (2010).
Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme.
Journal of the American Chemical Society, 132(36):12587–12596.

Bondar AN, Smith JC, and Elstner M (2010).
Mechanism of a Proton Pump Analyzed with Computer Simulations.
Theoretical Chemistry Accounts, 125(3-6):353-363.

Daidone I, Neuweiler H, Doose S, Sauer M, and Smith JC (2010).
Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains.
PLoS Computational Biology, 6(1):e1000645.

Glass D, Krishnan M, Nutt D, and Smith JC (2010).
Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models.
Journal of Chemical Theory and Computation, 6(4):1390-1400.

Guan Y, Ranoa DRE, Jiang S, Mutha S, Li X, Baudry J, and Tapping RI (2010).
Human TLRs 10 and 1 Share Common Mechanisms of Innate Immune Sensing but Not Signaling.
The Journal of Immunology, 184(9):5094-5103.

Guo HB, Johs A, Parks JM, Oliff L, Miller SM, Summers AO, Liang L, and Smith JC (2010).
Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg(II).
Journal of Molecular Biology, 398(4):555-568.

Johnson Q, Doshi U, Shen T, and Hamelberg D (2010).
Water’s Contribution to the Energetic Roughness from Peptide Dynamics.
Journal of Chemical Theory and Computation, 6(9):2591-2597.

Lopez M, Kurkal-Siebert V, Dunn RV, Tehei M, Finney JL, Smith JC, and Daniel RM (2010).
Activity and Dynamics of an Enzyme, Pig Liver Esterase, in Near-Anhydrous Conditions.
Biophysical Journal, 99(8):L62-L64.

Lu B, Cheng X, Huang J, and McCammon J (2010).
AFMPB: An Improved Poisson-Boltzmann Solver Using an Adaptive Fast Multipole Method.
Computer Physics Communications, 181(6):1150-1160.

Lynch RM, Rong R, Li B, Shen T, Honnen W, Mulenga J, Allen S, Pinter A, Gnanakaran S, and Derdeyn CA (2010).
Subtype-Specific Conservation of Isoleucine 309 in the Envelope V3 Domain is Linked to Immune Evasion in Subtype C HIV-1 Infection.
Virology, 404(1):59-70.

Moritsugu K, Njunda BM, and Smith JC (2010).
Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding.
Journal of Physical Chemistry B, 114(3):1479–1485.

Parks JM, Imhof P, and Smith JC (2010).
Understanding Enzyme Catalysis Using Computer Simulation.
In: Encyclopedia of Catalysis, ed. by IT Horváth. Wiley, chap. ?, pp. 1-45. (ISBN: 9780471227618).

Saharay M, Guo H, and Smith JC (2010).
Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS.
PLos ONE, 5(10):e12947.

Ulmschneider MB, Doux JPF, Killian JA, Smith JC, and Ulmschneider JP (2010).
Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides.
Journal of the American Chemical Society, 132(10):3452–3460.

Ulmschneider MB, Smith JC, and Ulmschneider JP (2010).
Peptide Partitioning Properties from Direct Insertion Studies.
Biophysical Journal, 98(12):L60-L62.

Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TYS, Martin SL, Guo HB, Smith JC, and Brown SD (2010).
A Paradigm for Strain Improvement Identifies Sodium Acetate Tolerance Loci in Zymomonas mobilis and Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences USA, 107(23):10395-10400.

Zahran M, Daidone I, Smith JC, and Imhof P (2010).
Mechanism of DNA Recognition by the Restriction Enzyme EcoRV.
Journal of Molecular Biology, 401(3):415-432.


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.

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.
SciDAC Review(15):34-45.

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 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.


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 SE, Soper AK, Daidone I, Smith JC, 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.

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.

Voltz K, Trylska J, Tozzini V, Kurkal-Siebert V, Langowski J, and Smith JC (2008).
Coarse-Grained Force Field for the Nucleosome from Self-Consistent Multiscaling.
Journal of Computational Chemistry, 29(9):1429-1439.


Bondar AN, Suhai S, Fischer S, Smith JC, and Elstner M (2007).
Suppression of the Back Proton-Transfer from Asp85 to the Retinal Schiff Base in Bacteriorhodopsin: A Theoretical Analysis of Structural Elements.
Journal of Structural Biology, 157(3):454–469.

Bondar AN, Suhai S, Smith JC, and Frangopol P (2007).
Computer Simulations of Local Anesthetic Mechanisms: Quantum Chemical Investigation of Procaine.
Romanian Reports in Physics, 59(2):289-299.

Cournia Z, Ullmann MG, and Smith JC (2007).
Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine Membrane: A Molecular Dynamics Simulation Study.
Journal of Physical Chemistry B, 111(7):1786–1801.

Daidone I, Ulmschneider MB, Di Nola A, Amadei A, and Smith JC (2007).
Dehydration-Driven Solvent Exposure of Hydrophobic Surfaces as a Driving Force in Peptide Folding.
Proceedings of the National Academy of Sciences USA, 104(39):15230–15235.

de Hatten X, Cournia Z, Huc I, Smith JC, and Metzler-Nolte N (2007).
Force-Field Development and Molecular Dynamics Simulations of Ferrocene-Peptide Conjugates as a Scaffold for Hydrogenase Mimics.
Chemistry - A European Journal, 13(29):8139–8152.

Guo HB, and Guo H (2007).
Mechanism of Histone Methylation Catalyzed by Protein Lysine Methyltransferase SET7/9 and Origin of Product Specificity.
Proceedings of the National Academy of Sciences USA, 104(21):8797–8802.

Koppole S, Smith JC, and Fischer S (2007).
The Structural Coupling between ATPase Activation and Recovery Stroke in the Myosin II Motor.
Structure, 15(7):825–837.

Meinhold L, Merzel F, and Smith JC (2007).
Lattice Dynamics of a Protein Crystal.
Physical Review Letters, 99(13):138101.

Meinhold L, Smith JC, Kitao A, and Zewail AH (2007).
Picosecond Fluctuating Protein Energy Landscape Mapped by Pressure Temperature Molecular Dynamics Simulation.
Proceedings of the National Academy of Sciences USA, 104(44):17261–17265.

Mesentean S, Koppole S, Smith JC, and Fischer S (2007).
The Principal Motions Involved in the Coupling Mechanism of the Recovery Stroke of the Myosin Motor.
Journal of Molecular Biology, 367(2):591–602.

Moritsugu K, and Smith JC (2007).
Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian.
Biophysical Journal, 93(10):3460–3469.

Noé F, and Smith JC (2007).
Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science.
In: Mathematical Modeling of Biological Systems, Volume I, ed. by A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel, chap. 11, pp. 121–137, Birkhäuser Boston. (ISBN: 978-0-8176-4557-1 (Print) 978-0-8176-4558-8 (Online)).

Noé F, Horenko I, Schütte C, and Smith JC (2007).
Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States.
Journal of Chemical Physics, 126(15):155102.

Nutt DR, and Smith JC (2007).
Choosing an Appropriate Water Model for Use in Biomolecular Simulations.
In: Physics and Chemistry of Ice, ed. by Kuhs, W. F., pp. 451-458, RSC Publishing.

Nutt DR, and Smith JC (2007).
Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?
Journal of Chemical Theory and Computation, 3(4):1550–1560.

Xu Q, Guo HB, Gorin A, and Guo H (2007).
Stabilization of a Transition-State Analogue at the Active Site of Yeast Cytosine Deaminase: Importance of Proton Transfers.
Journal of Physical Chemistry B, 111(23):6501–6506.

Xu Q, Guo HB, Wlodawer A, Nakayama T, and Guo H (2007).
The QM/MM Molecular Dynamics and Free Energy Simulations of the Acylation Reaction Catalyzed by the Serine-Carboxyl Peptidase Kumamolisin-As.
Biochemistry, 46(12):3784–3792.


Balog E, Smith JC, and Perahia D (2006).
Conformational Heterogeneity and Low-Frequency Vibrational Modes of Proteins.
Physical Chemistry Chemical Physics, 8:5543-5548.

Baudry J (2006).
Van der Waals Interactions and Decrease of the Rotational Barrier of Methyl-size Rotators: A Theoretical Study.
Journal of the American Chemical Society, 128(34):11088-11093.

Bondar AN, Smith JC, and Fischer S (2006).
Structural and Energetic Determinants of Proton Transfer in Bacteriorhodopsin.
Photochemical and Photobiological Sciences, 5:547-552.

Efferth T, Schwarzl SM, Smith JC, and Osieka R (2006).
Role of Glucose-6-Phosphate Dehydrogenase for Oxidative Stress and Apoptosis.
Cell Death and Differentiation, 13:527-528.

Guo H, Wlodawer A, Nakayama T, Xu Q, and Guo H (2006).
Catalytic Role of Proton Transfers in the Formation of a Tetrahedral Adduct in a Serine Carboxyl Peptidase.
Biochemistry, 45(30):9129–9137.

Imhof P, Noé F, Fischer S, and Smith JC (2006).
AM1/d Parameters for Magnesium in Metalloenzymes.
Journal of Chemical Theory and Computation, 2(4):1050–1056.

Koppole S, Smith JC, and Fischer S (2006).
Simulations of the Myosin II Motor Reveal a Nucleotide-State Sensing Element that Controls the Recovery Stroke.
Journal of Molecular Biology, 361(3):604-616.

Kurkal-Siebert V, and Smith JC (2006).
Low-Temperature Protein Physics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K.
Journal of the American Chemical Society, 128(7):2356-2364.

Kurkal-Siebert V, Daniel R, Finney JL, Tehei M, Dunn RV, and Smith JC (2006).
Enzyme Hydration, Activity and Flexibility: A Neutron Scattering Approach.
Journal of Noncrystalline Solids, 352(42-49):4387-4393.

Mesentean S, Fischer S, and Smith JC (2006).
Analyzing Large-Scale Structural Change in Proteins: Comparison of Principal Component Projection and Sammon Mapping.
Proteins: Structure, Function and Bioinformatics, 64(1):210-218.

Moritsugu K, and Smith JC (2006).
Temperature-Dependent Protein Dynamics: A Simulation-Based Probabilistic Diffusion-Vibration Langevin Description.
The Journal of Physical Chemistry B, 110(11):5807–5816.

Noé F, Krachtus D, Smith JC, and Fischer S (2006).
Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins.
Journal of Chemical Theory and Computation, 2(3):840-857.

Noé F, Oswald M, Reinelt G, Fischer S, and Smith JC (2006).
Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the αL ↔ β ↔ αR Transitions in Octaalanine.
Journal of Multiscale Modelling and Simulation, 5(2):393-419.

Schwarzl SM, Smith JC, and Fischer S (2006).
Insights into the Chemomechanical Coupling of the Myosin Motor from Simulation of its ATP Hydrolysis Mechanism.
Biochemistry, 45(18):5830-5847.

Smith JC (2006).
Tight in Titin.
Structure, 14(3):389-390.

Smith JC, Becker T, Fischer S, Noé F, Tournier AL, Ullmann GM, and Kurkal V (2006).
Physical and Functional Aspects of Protein Dynamics.
In: Soft Condensed Matter Physics in Molecular and Cell Biology, ed. by W.C.K. Poon and D. Andelman. Taylor & Francis, chap. 12, pp. 225-241. (ISBN: 978-0750310239).

Tehei M, Smith JC, Monk C, Ollivier J, Öttl M, Kurkal V, Finney JL, and Daniel RM (2006).
Dynamics of Immobilized and Native Escherichia coli Dihydrofolate Reductase by Quasieleastic Neutron Scattering.
Biophysical Journal, 90(3):1090-1097.

Walewski L, Krachtus D, Fischer S, Smith JC, Bala P, and Lesyng B (2006).
SCC-DFTB Energy Barriers for Single and Double Proton Transfer Processes in the Model Molecular Systems Malonaldehyde and Porphycene.
International Journal of Quantum Chemistry, 106(3):636-640.

Xu Q, Guo HB, Wlodawer A, and Guo H (2006).
The Importance of Dynamics in Substrate-Assisted Catalysis and Specificity.
Journal of the American Chemical Society, 128(18):5994–5995.


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