A. Navid, Y. Jiao, S. E. Wong, J. Pett-Ridge (2019) System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustrisBMC Bioinformatics, In press.


M. Griesemer, J. A. Kimbrel, C. E. Zhou, A. Navid, P. D’haeseleer (2018) Combining multiple functional annotation tools increases coverage of metabolic annotationBMC Genomics19, (1), 948.

H. Y. H. Tang, D. S. Shin, G. L. Hura, Y. Yang, X. Hu, F. C. Lightstone, M. D. McGee, H. S. Padgett, S. M. Yannone, and J. A. Tainer (2018) Structural control of nonnative ligand binding in engineered mutants of phosphoenolpyruvate carboxykinaseBiochemistry,  57, (48), 6688–6700.

S. Thallmair, H. I. Ingólfsson and S. J. Marrink (2018) Cholesterol flip-flop impacts domain registration in plasma membrane models. J. Phys. Chem. Lett.9, (18) 5527-5533.

T. S. Carpenter, C. A. López, C. Neale, C. Montour, H. I. Ingólfsson, F. Di Natale, F. C. Lightstone, and S. Gnanakaran (2018) Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force FieldJournal of Chemical Theory and Computation, 14, (11) 6050-6062.

J. M. Witkin, R. A. Shenvi, X. Li, S. D. Gleason, J. Weiss, D. Morrow, J. T. Catow, M. Wakulchik, M. Ohtawa, H-H. Lu, M. D. Martinez, J. M. Schkeryantz, T. S. Carpenter, F. C. Lightstone, R. Cerne (2018) Pharmacological characterization of the neurotrophic sesquiterpene jiadifenolide reveals a non-convulsant signature and potential for progression in neurodegenerative disease studiesBiochemical Pharmacology, 155, 61-70.

S. F. Gilmore, T. S. Carpenter, H. I. Ingolfsson, S. K. G. Peters, P. T. Henderson, C. D. Blanchette, N. O. Fischer (2018) Lipid composition dictates serum stability of reconstituted high-density lipoproteins: implications for in vivo applicationsNanoscale 10, 7420-7430.

J. P. Cranford, T. J. O’Hara, C. T. Villongco, O. M. Hafez, R. C. Blake, J. Loscalzo, J.-L. Fattebert, D. F. Richards, X. Zhang, J. N. Glosli, A. D. McCulloch, D. E. Krummen, F. C. Lightstone, S. E. Wong (2018) Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study. Cardiovascular Engineering and Technology 9, (3) 447-467.


H. I. Ingólfsson, T. S. Carpenter, H. Bhatia, P.-T. Bremer, S. J. Marrink, and F. C. Lightstone (2017) Computational lipidomics of the neuronal plasma membraneBiophysics Journal 113 (10), 2271-2280.

M. A Malfatti, H. A. Enright, N. A. Be, E. A. Kuhn, S. Hok, M. W. NcNerney, V. Lao, T. H. Nguyen, F. C. Lightstone, T. S. Carpenter, B. J. Bennion, C. A. Valdez (2017) The biodistribution and pharmacokinetics of the oxime acetylcholinesterase reactivator RS194B in guinea pigsChemico-Biological Interactions277, 159-167.

F. Qian, C. Huang, Y.-D. Lin, A. N. Ivanovskaya, T. J. O'Hara, R. H. Booth, C. J. Creek, H. A. Enright, D. A. Soscia, A. M. Belle, R. Liao, F. C. Lightstone, K. S. Kulp and E. K. Wheeler (2017) Simultaneous electrical recording of cardiac electrophysiology and contraction on chip.  Lab on a Chip 17, 1732-1739.

B. J. Bennion, N. A. Be, M. W. McNerney, V. Lao, E. M. Carlson, C. A. Valdez, M. A. Malfatti, H. A. Enright, T. H. Nguyen, F. C. Lightstone, and T. S Carpenter (2017) Predicting a Drug’s Membrane Permeability: A Computational Model Validated With In Vitro Permeability Assay Data.  J. Phys. Chem. B 121 (20), 5228-5237.

M. C. Yung, F. A. Bourguet, T. S. Carpenter, M. A. Coleman (2017) Re-directing bacterial microcompartment systems to enhance recombinant expression of lysis protein E from bacteriophage ϕX174 in Escherichia coliMicrob. Cell Fact. 16 (71).

X. Zhang, H. Perez-Sanchez, F. C. Lightstone (2017) A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding AntithrombinCurrent Topics in Medicinal Chemistry 17, 1-9.


T. Carpenter, J. Parkin, and S. Khalid (2016) The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile. J. Phys. Chem. Lett(17), 3446-3451.

S. Witzke, M. Petersen, T. Carpenter, S. Khalid (2016) Molecular dynamics simulations reveal the conformational flexibility of Lipid II and its loose association with the defensin plectasin in the Staphylococcus aureus membrane. Biochemistry 55(23): 3303-3314.

T. C. Ramalho, A. A. de Castro, D. R. Silva, M C. Silva, T. C. C. Franca, B. J. Bennion and K. Kuca (2016) Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches toward Remediation Technologies of Warfare Agents and Pesticides. Current Medicinal Chemistry 23, 1041-1061.

T. S. Carpenter and F. C. Lightstone (2016) An Electrostatic Funnel in the GABA-Binding Pathway. PLoS Comput. Biol., 12(4): e1004831.

T. A. Pham, S. M. G. Mortuza, B. C. Wood, E. Y. Lau, T. Ogitsu, S. F. Buchsbaum, Z. S. Siwy, F. Fornasiero, and E. Schwegler (2016) Salt Solutions in Carbon Nanotubes: The Role of Cation−π InteractionsJ. Phys. Chem. C 120 (13), 7332–7338.

B. P. Mayer, D. J. Kennedy, E. Y. Lau, C. A. Valdez (2016) Solution-State Structure and Affinities of Cyclodextrin:Fentanyl Complexes by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics SimulationJ. Phys. Chem. B 120(9), 2423-2433.

A. Navid, D. M. Ng, S. E. Wong, F. C. Lightstone (2016) Application of a physiologically-based pharmacokinetic model to study theophylline metabolism and its interactions with ciprofloxacin and caffeine. CPT: Pharmacometrics & Systems Pharmacology, 5 (2), 74-81.

E. Y. Lau, M. L. Berkowitz, E. Schwegler (2016) Shock Wave-Induced Damage of a Protein by Void Collapse. Biophysical Journal, 110, 1, 147–156.

R. A. Kelsey, D. A. Miller, S. R. Parkin, K. Liu, J. E. Remias, Y. Yang, F. C. Lightstone, K. Liu, C. A. Lippert, S. A. Odom, (2016) Carbonic Anhydrase Mimics for Enhanced CO2 Absorption in an Amine-Based Capture Solvent. Dalton Transactions, 45, 324-333.


J.-L. Fattebert, E. Y. Lau, B. J. Bennion, P. Huang, and F. C. Lightstone (2015)  Large-scale First-Principles molecular dynamics simulations with electrostatic embedding: application to acetylcholinesterase catalysis. J. Chem. Theory Comput., 11, 5688–5695. 

A. Ebrahim, E. Almaas, E. Bauer, A. Bordbar, A. P. Burgard, R. L. Chang, A. Dräger, I. Famili, A. M. Feist, R. M. T. Fleming, S. S. Fong, V. Hatzimanikatis, M. J. Herrgård, A. Holder, M. Hucka, D. Hyduke, N. Jamshidi, S. Y. Lee, N. Le Novère, J. A. Lerman, N. E. Lewis, D. Ma, R. Mahadevan, C. Maranas, H. Nagarajan, A. Navid, J. Nielsen, L. K. Nielsen, J. Nogales, A. Noronha, C. Pal, B. O. Palsson, J. A. Papin, K. R. Patil, N. D. Price, J. L. Reed, M. Saunders, R. S. Senger, N. Sonnenschein, Y. Sun, I. Thiele (2015) Do Genome-scale Models Need Exact Solvers or Clearer Standards?  Molecular Systems Biology, 11, 831.

B. J. Bennion, S. G. Essiz, E. Y. Lau, J.-L. Fattebert, A. Emigh, F. C. Lightstone (2015) A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations. PLoS ONE, 10(4): e0121092.

X. Zhang, H. Péréz-Sánchez, and F. C. Lightstone. (2015) Molecular Dynamics Simulations of Ligand Recognition Upon Binding Antithrombin: A MM/GBSA Approach. Bioinformatics and Biomedical Engineering, 9044, 584-593.

S. P. Hau-Riege and B. J. Bennion (2015) Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulsesPhys Rev E91(2), 022705.


M. X. LaBute, X. Zhang, J. Lenderman, B. J. Bennion, S. E. Wong, F. C. Lightstone (2014) Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines. PLoS ONE, 9(9): e106298.

T. S. Carpenter, D. A. Kirshner, E. Y. Lau, S. E. Wong, J. P. Nilmeier, and F. C. Lightstone (2014) A Method to Predict Blood-Brain Barrier Permeability of Drug-like Compounds Using Molecular Dynamics SimulationsBiophys. J., 107(3), 630-641.

C. Zhao, S. H. Hwang, B. A. Buchholz , T. S. Carpenter, F. C. Lightstone, J. Yang, B. D. Hammock, J. E. Casida (2014) The GABAA Receptor Target of Tetramethylenedisulfotetramine. Proc. Natl. Acad. Sci. USA, 111(23), 8607-8612.

Y. Yang, S. E. Wong and F. C. Lightstone (2014) Understanding a Substrate’s Product Regioselectivity in a Family of Enzymes:  A Case Study of Acetaminophen Binding in Cytochrome P450s. PLoS ONE, 9(2): e87058.

H. J. Kulik, S. E. Wong, S. E. Baker, C. A. Valdez, J. H. Satcher, R. D. Aines, and F. C. Lightstone (2014) Developing an approach for first-principles catalyst design: application to carbon capture catalysis. Acta Crystallographica, C70, 123-131. 

X. Zhang, S. E. Wong, F. C. Lightstone (2014) Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment. J. Chem. Inf. Model., 54(1) 324-337.


L. W. Tari, X. Li, M. Trzoss, D. C. Bensen, Z. Chen, T. Lam, J. Zhang, S. J. Lee, G. Hough, D. Phillipson, S. Akers-Rodriguez, M. L. Cunningham, B. P. Kwan, K. J. Nelson, A. Castellano, J. B. Locke, V. Brown-Driver, T. M. Murphy, V. S. Ong, C. M. Pillar, D. L. Shinabarger, J. Nix, F. C. Lightstone, S. E. Wong, T. B. Nguyen, K. J. Shaw, J. Finn (2013) Tricyclic GyrB/ParE (TriBE) Inhibitors: A New Class of Broad-Spectrum Dual-Targeting Antibacterial AgentsPLoS ONE, 8(12): e84409.

L. Koziol, N. Kumar, S. E. Wong, F. C. Lightstone (2013) Molecular Recognition of Aromatic Rings by Flavin: Electrostatics and Dispersion Determine Ring Positioning Above Isoalloxazine. J. Phys. Chem. A, 117, 12946-12952. 

A. Navid, D. M. Ng, B. J. Stewart, S. E. Wong, and F. C. Lightstone (2013) Quantitative in silico analysis of transient metabolism of acetaminophen and associated causes of hepatotoxicity in humans. In Silico Pharmacology, 1, 14.

T. S. Carpenter, E. Y. Lau, and F. C. Lightstone (2013) Identification of a Possible Secondary Picrotoxin-Binding Site on the GABAA-Receptor. Chemical Research in Toxicology, 26, 1444-1454.

B. J. Bennion, E. Y.  Lau, J.-L. Fattebert, P. Huang, E. Schwegler, W. Corning, F. C. Lightstone (2013) Modeling the Binding of CWAs to AChE and BuChE. Military Medical Science Letters, vol. 82(3), 102-114.

E. Y. Lau, S. E. Wong, S. E. Baker, J. P. Bearinger, L. Koziol, C. A. Valdez, J. H. Satcher Jr, R. D. Aines and F. C. Lightstone (2013) Comparison and Analysis of Zinc and Cobalt-based Systems as Catalytic Entities for the Hydration of Carbon Dioxide. PLoS ONE, 8(6), e66187.

D. A. Kirshner, J. P. Nilmeier, and F. C. Lightstone (2013) Catalytic Site Identification – A Web Server to Identify Catalytic Site Structural Matches Throughout PDB. Nucleic Acids Research, 41, W256-W265

J. P. Nilmeier, D. A. Kirshner, S. E. Wong, and F. C. Lightstone (2013) Rapid Catalytic Template Searching as an Enzyme Function Prediction ProcedurePLoS ONE, 8(5), e62535.

P. R. Kumaresan, S. Devaraj, W. Huang, E. Y. Lau, R. Liu, K. S. Lam, I. Jialal (2013) Synthesis and characterization of a novel inhibitor of C-reactive protein-mediated proinflammatory effectsMetab. Synd.r Relat. Disord. 11(3),177-184.

S. Chaudhury, M. D. M. Abdulhameed, N. Singh, G. J. Tawa, P. M. D’haeseleer, A. T. Zemla, A. Navid, C. E. Zhou, M. C. Franklin, J. Cheung, M. J. Rudolph, J. Love, J. F. Graf, D. A. Rozak, J. L. Dankmeyer, K. Amemiya, S. Daefler, A. Wallqvist (2013) Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction. PLoS ONE 8(5), e63369.

X. Zhang, S. E. Wong, F. C. Lightstone (2013) Message Passing Interface and Multithreading Hybrid for Parallel Molecular Docking of Large Databases on Petascale High Performance Computing Machines. J. Comput. Chem., 34, 915-927.

L. Koziol, S. G. Essiz, S. E. Wong, E. Y. Lau, C. A. Valdez, J. H. Satcher, Jr., R. D. Aines, F. C. Lightstone (2013) Computational Analysis of a Zn-bound Tris(imidazolyl) Calix[6]arene Aqua Complex:  Toward Incorporating Second-coordination Sphere Effects into Carbonic Anhydrase Biomimetics. J. Chem. Theory. Comput., 9, 1320-1327.

Y. Yang, F. C. Lightstone, S. E. Wong (2013) Solvents in Structure-Based in Drug Discovery. Expert Opinion On Drug Discovery, 8, 277-287.

B. J. Stewart, A. Navid, K. S. Kulp, J. L. S. Knaack, and G. Bench (2013), D-Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae. Yeast, 30, 81–91.

M. Trzoss, D. C. Bensen, X. Li, Z. Chen, T. Lam, J. Zhang, C. J. Creighton, M. L. Cunningham, B. Kwan, M. Stidham, K. Nelson, V. Brown-Driver, A. Castellano, K. J. Shaw, F. C. Lightstone, S. E. Wong, T. B. Nguyen, J. Finn, L. W. Tari (2013) Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: Development of inhibitors with broad spectrum, Gram-negative antibacterial activityBioorg. Med. Chem. Lett., 23, 1537-1543.

L. W. Tari, M. Trzoss, D. C. Bensen, X. Li, Z. Chen, T. Lam, J. Zhang, C. J. Creighton, M. L. Cunningham, B. Kwan, M. Stidham, K. J. Shaw, F. C. Lightstone, S. E. Wong, T. B. Nguyen, J. Nix, J. Finn (2013) Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activityBioorg. Med. Chem. Lett., 23, 1529-1536.


A. Navid, E. Almaas (2012) Genome-Level Transcription Data of Yersina Pestis Analyzed With A New Metabolic Constraint-Based Approach. BMC Systems Biology, 6(1), 150.

T. S. Carpenter, E. Y. Lau and F. C. Lightstone (2012) A Role for Loop-F in Modulating GABA Binding Affinity in the GABAA Receptor. J. Mol. Bio., 422, 310-323.

CY. Jiao, A. Navid, B. J. Stewart, J. McKinlay, M. P. Thelen, J. Pett-Ridge (2012) Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum and Rhodopseudomonas palustris for hydrogen production. Int. J. Hydrogen Energy 37, 11719-11726.

L. Koziol, C. A. Valdez, S. E. Baker, E. Y. Lau, W. C. Floyd III, S. E. Wong, J. H. Satcher Jr., F. C. Lightstone, R. D. Aines (2012) Towards a small molecule, biomimetic carbonic anhydrase model: theoretical and experimental investigations of a panel of Zinc(II) aza-macrocyclic catalystsInorganic Chemistry51, 6803-6812.

A. Navid (2012) "Development of constraint-based system-level models of microbial metabolism" in Microbial Systems Biology, Methods in Molecular Biology, Vol. 881, ISBN: 9781617798269, ed. Navid, A., Chapter 18, 531-549.

W. H. Benner, G. S. Lewis, S. V. Hering, B. Segelke, M. Corzett, J. E. Evans and F. C. Lightstone (2012) Re-Electrospraying Splash-Landed Proteins and Nanoparticles. Analytical Chemistry, 84, 2498-2504.

A. Navid and E. Almaas (2012) "Yersinia pestis Metabolic Network" in Yersinia:  Systems Biology and Control, ISBN: 978-1-908230-05-8, eds. Carniel, E ; Hinnebusch, BJ; Caister Academic Press, Norfolk, UK, Chapter 6, 83-108.


A. Navid (2011) Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targetsBriefings in Functional Genomics10(6), 354-364.

J. H. Satcher Jr., S. E. Baker, H. J. Kulik, C. A. Valdez, R. L. Krueger, F. C. Lightstone, R. D. Aines (2011) Modeling, synthesis and characterization of zinc containing carbonic anhydrase active site mimics. Energy Procedia, 4, 2090-2095.

S. E. Wong, E. Y. Lau, H. J. Kulik, J. H. Satcher, C. Valdez, M. Worsely, F. C. Lightstone, R. D. Aines (2011) Designing small molecule catalysts for CO2 captureEnergy Procedia4, 817-823.

S. E. Wong and F. C. Lightstone (2011) Accounting for water molecules in drug designExpert Opinion On Drug Discovery6, 65-74.