2024
Tugba Nur Ozturk, Melanie König, Timothy S. Carpenter, Kasper B. Pedersen, Tsjerk A. Wassenaar, Helgi I. Ingólfsson, Siewert J. Marrink (2024) Building complex membranes with Martini 3. Methods in Enzymology.
Stephen J. Beckett, David Demory, Ashley R. Coenen, John R. Casey, Mathilde Dugenne, Christopher L. Follett, Paige Connell, Michael C. G. Carlson, Sarah K. Hu, Samuel T. Wilson, Daniel Muratore, Rogelio A. Rodriguez-Gonzalez, Shengyun Peng, Kevin W. Becker, Daniel R. Mende, E. Virginia Armbrust, David A. Caron, Debbie Lindell, Angelicque E. White, François Ribalet & Joshua S. Weitz (2024) Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre. Nature Communications 15, 2105.
Heesung Shim, Jonathan E. Allen, W.F. Drew Bennett (2024) Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures. Machine Learning and Knowledge Extraction 6(1), 642-657.
Lisa R. Moore, Ron Caspi, Douglas A. Campbell, John R. Casey, Sophie Crevecoeur, David J. Lea-Smith, Bin Long, Naaman M. Omar, Suzanne M. Paley, Nicolas M. Schmelling, Alejandro Torrado, Jonathan P. Zehr, and Peter D. Karp (2024) CyanoCyc cyanobacterial web portal. Frontiers in Microbiology 15:1340413.
2023
Austen Bernardi, W. F. Drew Bennett, Stewart He, Derek Jones, Dan Kirshner, Brian J. Bennion and Timothy S. Carpenter (2023) Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery. Membranes 13 851.
Garrett A. Stevenson, Dan Kirshner, Brian J. Bennion, Yue Yang, Xiaohua Zhang, Adam Zemla, Marisa W. Torres, Aidan Epstein, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Sergio E. Wong, Jonathan E. Allen, Felice C. Lightstone (2023) Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. Journal of Chemical Information and Modeling 63, 21, 6655-6666.
Helgi I. Ingólfsson, Azamat Rizuan, Xikun Liu, Priyesh Mohanty, Paulo C.T. Souza, Siewert J. Marrink, Michael T. Bowers, Jeetain Mittal, Joel Berry (2023) Multiscale simulations reveal TDP-43 molecular level interactions driving condensation. Biophysical Journal.
Ya Ju Fan, Jonathan E. Allen, Kevin S. McLoughlin, Da Shi, Brian J. Bennion, Xiaohua Zhang, Felice C. Lightstone (2023) Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction. Artificial Intelligence Chemistry 1 (1).
H. I. Ingólfsson, H. Bhatia, F. Aydin, T. Oppelstrup, C. A López, L. G. Stanton, T. S. Carpenter, S. Wong, F. Di Natale, X. Zhang, J. Y. Moon, C. B. Stanley, J. R. Chavez, K. Nguyen, G. Dharuman, V. Burns, R. Shrestha, D. Goswami, G. Gulten, Q. N. Van, A. Ramanathan, B. Van Essen, N. W. Hengartner, A. G. Stephen, T. Turbyville, P.-T. Bremer, S. Gnanakaran, J. N. Glosli, F. C. Lightstone, D. V. Nissley, F. H. Streitz (2023) Machine Learning-driven Multiscale Modeling: Bridging the Scales With a Next Generation Simulation Infrastructure. J. Chem. Theory Comput. 19 (9), 2658-2675.
H. Bhatia, F. Aydin, T. S. Carpenter, F. C. Lightstone, P.-T. Bremer, H. I. Ingólfsson, D. V. Nissley, F. H. Streitz (2023) The confluence of machine learning and multiscale simulations. Current Opinion in Structural Biology, 80, 102569.
Kyllo T, Singh V, Shim H, Latika S, Nguyen HM, Chen YJ, Terry E, Wulff H, Erickson JD (2023) Riluzole and novel naphthalenyl substituted aminothiazole derivatives prevent acute neural excitotoxic injury in a rat model of temporal lobe epilepsy. Neuropharmacology, 224,109349.
L. G. Stanton, T. Oppelstrup, T. S. Carpenter, H. I. Ingólfsson, M. P. Surh, F. C. Lightstone, J. N. Glosli (2023) Dynamic density functional theory of multicomponent cellular membranes. Physical Review Research, 5, 013080.
E. VanArsdale, A. Navid, M. J. Chu, T. M. Halvorsen, G. F. Payne, Y. Jiao, W. E. Bentley, M. C. Yung (2023). Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis. Biotechnology and Bioengineering, 1-16.2022
A. Zemla, J. E. Allen, D. Kirshner, F. C Lightstone (2022) PDBspheres – a method for finding 3D similarities in local regions in proteins. NAR Genomics and Bioinformatics, 4, 4, lqac078.
D. H. Ahn, X. Zhang, J. Mast, S. Herbein, F. Di Natale, D. Kirshner, S. A. Jacobs, I. Karlin, D. J. Milroy, B. R. De Supinski, B. Van Essen, J. Allen, F. C. Lightstone (2022) Scalable Composition and Analysis Techniques for Massive Scientific Workflows, Proceedings of the 18th IEEE International Conference on e-Science (e-Science), Salt Lake City, UT, USA, 32-42. (Won Best Paper)
X. Zeng, F. Wang, Y. Luo, S.-g. Kang, J. Tang, F. C. Lightstone, E. F. Fang, W. Cornell, R. Nussinov, F. Cheng (2022) Deep Generative Molecular Design Reshapes Drug Discovery. Cell Reports Medicine, 3, 100794.
K. Nguyen, C. A. López, C. Neale, Q. N. Van, T. S. Carpenter, F. Di Natale, T. Travers, T. H. Tran, A. H. Chan, H. Bhatia, P. H. Frank, M. Tonelli, X. Zhang, G. Gulten, T.Reddy, V. Burns, T. Oppelstrup, N. Hengartner, D. K. Simanshu, P.-T. Bremer, D. Chen, J. N. Glosli, R. Shrestha, T. Turbyville, F. H. Streitz, D. V. Nissley, H. I. Ingólfsson, A. G. Stephen, F. C. Lightstone, S. Gnanakaran (2022) Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys. J., 121, 19, 3630.
H. Bhatia, J. J. Thiagarajan, R. Anirudh, T. S. Jayram, T. Oppelstrup, H. I. Ingólfsson, F. C. Lightstone, P.-T. Bremer (2022) A Biology-Informed Similarity Metric for Simulated Patches of Human Cell Membrane. Machine Learning: Science and Technology, 3 (3), 2632-2153.
M. Windler, R. Stuart, J. S. Deutzmann, X. Mayali, A. Navid, P. D’haeseleer, O. E. Marcu, M. Lipton, C. Nicora, A. M. Spormann (2022) Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity. FEMS Microbiology Ecology, 98, 1.
S. Conti, E. Y. Lau, and V. Ovchinnikov (2022) On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations. Antibodies, 11(3), 51.
C. A. Lopez, X. Zhang, F. Aydin, R. Shrestha, Q. N. Van, C. B. Stanley, T. S. Carpenter, K. Nguyen, L. A. Patel, D. Chen, V. Burns, N. W. Hengartner, T. J. E. Reddy, H. Bhatia, F. Di Natale, T. H. Tran, A. H. Chan, D. K. Simanshu, D. V. Nissley, F. H. Streitz, A. G. Stephen, T. J. Turbyville, F. C. Lightstone, S. Gnanakaran, H. I Ingolfsson, C. Neale (2022) Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J. Chem. Theory Comput., 18 (8), 5025-5045.
F. Zhu, F. A. Bourguet, W. F. D. Bennett, E. Y. Lau, K. T. Arrildt, B. W. Segelke, A. T. Zemla, T. A. Desautels, and D. M. Faissol (2022) Large-scale application of free energy perturbation calculations for antibody design. Scientific Reports 12, 12489.
W. F. D. Bennett, S. J. Fox, D. Sun, and C. M. Maupin (2022) Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules. Membranes 12, 4, 350.
A. M. Maer, R. Rusinova, L. L. Providence, H. I. Ingólfsson, S. A. Collingwood, J. A. Lundbæk, O. S. Andersen (2022) Regulation of Gramicidin Channel Function Solely by Changes in Lipid Intrinsic Curvature. Frontiers in Physiology, 13:836789.
W. Martin, G. Sheynkman, F. C. Lightstone, R. Nussinov, F. Cheng (2022) Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease. Current Opinion in Structural Biology, 72, 103.
G. C. Egan, E. Y. Lau, and E. Schwegler (2022) Multiframe Imaging of Micron and Nanoscale Bubble Dynamics. Nano Letters, 22 (3), 1053-1058.
H. I. Ingólfsson, C. Neale, T. S. Carpenter, R. Shrestha, C. A. López, T. H. Tran, T. Oppelstrup, H. Bhatia, L. G. Stanton, X.Zhang, S. Sundram, F. Di Natale, A. Agarwal, G. Dharuman, S. I. L. Kokkila Schumacher, . Turbyville, G. Gulten, Q. N. Van, D. Goswami, F. Jean-Francois, C. Agamasu, D. Chen, J. J. Hettige, T. Travers, S. Sarkar, M. P. Surh, Y. Yang, A. Moody, S. Liu, B. C. Van Essen, A. F. Voter, A. Ramanathan, N.W. Hengartner, D. K. Simanshu, A. G. Stephen, P.-T. Bremer, S. Gnanakaran, J. N. Glosli, F. C. Lightstone, F. McCormick, D. V. Nissley, and F. H. Streitz (2022) Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins. Proceedings of the National Academy of Sciences, 119 (1) e2113297119.
2021
H. Bhatia, F. Di Natale, J. Y. Moon, X. Zhang, J. R. Chavez, F. Aydin, C. Stanley, T. Oppelstrup, C. Neale, S. Kokkila Schumacher, D. H. Ahn, S. Herbein, T. S. Carpenter, S. Gnanakaran, P.-T. Bremer, J. N. Glosli, F. C. Lightstone, H. I. Ingólfsson (2021) Generalizable coordination of large multiscale workflows: challenges and learnings at scale. SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Article No.: 10, 1-16.
G. A. Stevenson, D. Jones, H. Kim, W. F. D. Bennett, B. J. Bennion, M. Borucki, F. Bourguet, A. Epstein, M. Franco, B. Harmon, S. He, M. P. Katz, D. Kirshner, V. Lao, E. Y. Lau, J. Lo, K. McLoughlin, R. Mosesso, D. K. Murugesh, O. A. Negrete, E. A. Saada, B. Segelke, M. Stefan, M. W. Torres, D. Weilhammer, S. Wong, Y. Yang, A. Zemla, X. Zhang, F. Zhu, F. C. Lightstone, J. E. Allen (2021) High-throughput virtual screening of small molecule inhibitors for SARS-CoV-2 protein targets with deep fusion models. SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Article No.: 74, 1–13.
J.S. Yeom, K. Georgouli, R. Blake, A. Navid (2021) Towards dynamic simulation of a whole cell model. BCB '21: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Article No.: 82, 1-10.
B. J. Bennion, M. A. Malfatti, N. A. Be, H. A. Enright, S. Hok, C. L. Cadieux, T. S. Carpenter, V. Lao, E.A. Kuhn, M.W. McNerney, F. C. Lightstone, T. H. Nguyen, and C.A. Valdez (2021) Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach. Scientific Reports, 11, 15567.
E. Y. Lau, O. A. Negrete, W. F. D.Bennett, B. J. Bennion, M. Borucki, F. Bourguet, A. Epstein, M. Franco, B. Harmon, S. He, D. Jones, H. Kim, D. Kirshner, V. Lao, J. Lo, K. McLoughlin, R. Mosesso, D. K. Murugesh, E. A. Saada, B. Segelke, M. A. Stefan, G. A. Stevenson, M. W. Torres, D. R. Weilhammer, S. Wong, Y. Yang, A. Zemla, X. Zhang, F. Zhu, J. E. Allen, F. C. Lightstone (2021) Discovery of Small-molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline. Frontiers in Molecular Biosciences, 8, 644.
S. A. Jacobs, T. Moon, K. McLoughlin, D. Jones, D. Hysom, D. H. Ahn, J. Gyllenhaal, P. Watson, F. C. Lightstone, J. E. Allen, I. Karlin, B. Van Essen (2021) Enabling Rapid COVID-19 Small Molecule Drug Design Through Scalable Deep Learning of Generative Models. International Journal of High Performance Computing Applications, 35(5), 469–482.
H. Bhatia, T. Carpenter , H. Ingolfsson , G. Dharuman , P. Karande , S. Liu , T. Oppelstrup , C. Neale , F. Lightstone , B. Van Essen , J. Glosli , P.-T. Bremer (2021) Machine Learning Based Dynamic-Importance Sampling for Adaptive Multiscale Simulations. Nature Machine Intelligence, 3, 401–409. https://doi.org/10.1038/s42256-021-00327-w.
D. Jones, H. Kim, X. Zhang, A. Zemla, G. Stevenson, W. F. D. Bennett, D. Kirshner, S. E. Wong, F. C. Lightstone, and J. E. Allen (2021) Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. J. Chem. Info. Model., 61, 4, 1583–1592.
F. Cheng, J. Zhao, Y. Wang, W. Lu, Z. Liu, Y. Zhou, W. Martin, R. Wang, J. Huang, T. Hao, H. Yue, J. Ma, Y. Hou, J. Castrillon, J. Fang, J. Lathia, R. A. Keri, F. C. Lightstone, E. M. Antman, R. Rabadan, D. E. Hill, C. Eng, M. Vidal, J. Loscalzo (2021) Comprehensive characterization of protein-protein interaction network perturbations by human disease mutations. Nature Genetics, 53, 342–353.
D. Sun, S. He, W. F. D. Bennett, C. L. Bilodeau,O. S. Andersen, F. C. Lightstone, H. I. Ingolfsson (2021) Atomistic Characterization of Gramicidin Channel Formation. J. Chem. Theory Comput., 17, 1, 7–12.
2020
D. H. Ahn, N. Bass, A. Chu, J. Garlick, M. Grondona, S. Herbein, H. I. Ingólfsson, J. Koning, T. Patki, T. R. W. Scogland, B. Springmeyer and M. Taufer. (2020) Flux: Overcoming Scheduling Challenges for Exascale Workflows. Future Generation Computer Systems, 110, 202-213.
D. Sun, T. A. Peyear, W. F. D. Bennett, M. Holcomb, S. He, F. Zhu, F. C. Lightstone, O. S. Andersen and Helgi I. Ingólfsson (2020) Assessing the Perturbing Effects of Drugs on Lipid Bilayers using Gramicidin Channel-Based in Silico and in Vitro Assays. J. Med. Chem. 63, 11809-11818.
W. F. D. Bennett, S. He, C. L. Bilodeau, D. Jones, D. Sun, H. Kim, J. E. Allen, F. C. Lightstone, H. I. Ingolfsson (2020) Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning. J. Chem. Inf. Model., 60, 11, 5375-5381.
H. I. Ingólfsson, H. Bhatia, T. Zeppelin, W. F. D. Bennett, K. A. Carpenter, P.-C. Hsu, G. Dharuman, P.-T. Bremer, B. Schiøtt, F. C. Lightstone, and T. S. Carpenter (2020) Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity. J. Phys. Chem. B, 124, 36, 7819–7829.
M. Blumer, S. Harris, M. Li, L. Martinez, M. Untereiner, P. N. Saeta, T. S. Carpenter, H. I. Ingólfsson and W. F. D Bennett. (2020) Simulations of asymmetric membranes illustrate cooperative leaflet coupling and lipid adaptability. Frontiers Cell Developmental Biology, 8, 575.
X. Zhang, S. Sundram, T. Oppelstrup, S. I. L. Kokkila-Schumacher, T. S. Carpenter, H. I. Ingolfsson, F. H. Streitz, F. C. Lightstone, J. N. Glosli (2020) ddcMD:A Fully GPU-accelerated Molecular Dynamics Program for the Martini Force Field. J. Chem. Phys., 153, 045103.
F. Zhu, X. Zhang, J. E. Allen, D. Jones, F. C. Lightstone (2020) Binding Affinity Prediction by Pairwise Function Based on Neural Network. J. Chem. Inf. Model. 60, 2766-2772.
J. A. Hammons, H. I. Ingólfsson, J. R. I. Lee, T. S. Carpenter, J. Sanborn, R. Tunuguntla, Y. C. Yao, T. M. Weiss, A. Noy, T. Van Buuren. (2020) Decoupling copolymer, lipid and carbon nanotube interactions in hybrid, biomimetic vesicles. Nanoscale, 12, 6545-6555.
W. R. Martin, F. C. Lightstone, F. Cheng (2020) In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR Complex. International Journal of Molecular Sciences. 21(5), 1550.
V. Ovchinnikov, S. Conti, E. Y. Lau, F. C. Lightstone, M. Karplus (2020) Microsecond molecular dynamics simulations of proteins using a quasi-equilibrium solvation shell model. J. Chem. Theory Comput., 16, 3, 1866–1881.
D. Goswami, D. Chen, Y. Yang, P. R. Gudla, J. Columbus, K. Worthy, M. Rigby, M. Wheeler, S. Mukhopadhyay, K. Powell, W. Burgan, V. Wall, D. Esposito, D. Simanshu, F. C. Lightstone, D. V. Nissley, F. McCormick, T. Turbyville (2020) Membrane Interactions of the G-domain and the HVR of KRAS4b Defines Its Unique Diffusion Behavior. eLife, 9: e47654.
2019
F. Di Natale, H. Bhatia, T. S. Carpenter, C. Neale, S. Kokkila Schumacher, T. Oppelstrup, L. Stanton, X. Zhang, S. Sundram, T. R. W. Scogland, G. Dharuman, M. P. Surh, Y. Yang, C. Misale, L. Schneidenbach, C. Costa, C. Kim, B. D’Amora, S. Gnanakaran, D. V. Nissley, F. Streitz, F. C. Lightstone, P.-T. Bremer, J. N. Glosli, H. I. Ingolfsson (2019) A Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer. SC '19: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Article No.: 57, 1–16. (won Best Paper)
D. Sun, T. A. Peyear, W. F. D. Bennett, O. S. Andersen, F. C. Lightstone, H. I. Ingolfsson (2019) Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness. Biophys. J., 117, 1831–1844.
H. Bhatia, H. I. Ingolfsson, T. S. Carpenter, F. C. Lightstone, P.-T. Bremer (2019) MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes. J. Chem.Theory Comput., 15, 11, 6411-6421.
R.G. Huber, T.S. Carpenter, N. Dube, D.A. Holdbrook, H.I. Ingólfsson, W.A. Irvine, J.K. Marzinek, F. Samsudin, J.R. Allison, S. Khalid, and P.J. Bond (2019) Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions In: Kleinschmidt J. (eds) Lipid-Protein Interactions. Methods in Molecular Biology, vol 2003 (2019). Humana, New York, NY.
A. Navid, Y. Jiao, S. E. Wong, J. Pett-Ridge (2019) System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris. BMC Bioinformatics, 20:233.
2018
M. Griesemer, J. A. Kimbrel, C. E. Zhou, A. Navid, P. D’haeseleer (2018) Combining multiple functional annotation tools increases coverage of metabolic annotation. BMC Genomics, 19, (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 carboxykinase. Biochemistry, 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 Field. Journal 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 studies. Biochemical 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 applications. Nanoscale 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.
2017
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 membrane. Biophysics 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 pigs. Chemico-Biological Interactions, 277, 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 coli. Microb. 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 Antithrombin. Current Topics in Medicinal Chemistry 17, 1-9.
2016
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. 7 (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 Interactions. J. 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 Simulation. J. 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.
2015
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 pulses. Phys Rev E, 91(2), 022705.
2014
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 Simulations. Biophys. 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.
2013
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 Agents. PLoS 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 Procedure. PLoS 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 effects. Metab. 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 activity. Bioorg. 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 activity. Bioorg. Med. Chem. Lett., 23, 1529-1536.
2012
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 catalysts. Inorganic Chemistry. 51, 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.
2011
A. Navid (2011) Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets. Briefings in Functional Genomics, 10(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 capture. Energy Procedia, 4, 817-823.
S. E. Wong and F. C. Lightstone (2011) Accounting for water molecules in drug design. Expert Opinion On Drug Discovery, 6, 65-74.