• 2351 Citations
  • 27 h-Index
1994 …2020

Research output per year

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Research Output

  • 2351 Citations
  • 27 h-Index
  • 76 Article
  • 4 Conference contribution
  • 1 Chapter
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Article
2020

Binding Affinity Prediction by Pairwise Function Based on Neural Network

Zhu, F., Zhang, X., Allen, J. E., Jones, D. & Lightstone, F. C., Jan 1 2020, (Accepted/In press) In : Journal of Chemical Information and Modeling.

Research output: Contribution to journalArticle

In silico insights into protein–protein interaction disruptive mutations in the PCSK9-LDLR complex

Martin, W. R., Lightstone, F. C. & Cheng, F., Mar 1 2020, In : International journal of molecular sciences. 21, 5, 1550.

Research output: Contribution to journalArticle

Open Access

Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior

Goswami, D., Chen, D., Yang, Y., Gudla, P., Columbus, J., Worthy, K., Rigby, M., Wheeler, M., Mukhopadhyay, S., Powell, K., Burgan, W., Wall, V., Esposito, D., Simanshu, D., Lightstone, F., Nissley, D. V., McCormick, F. & Turbyville, T., Jan 2020, In : eLife. 9, e47654.

Research output: Contribution to journalArticle

Open Access

Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

Ovchinnikov, V., Conti, S., Lau, E. Y., Lightstone, F. C. & Karplus, M., Mar 10 2020, In : Journal of Chemical Theory and Computation. 16, 3, p. 1866-1881 16 p.

Research output: Contribution to journalArticle

2019

MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes

Bhatia, H., Ingólfsson, H. I., Carpenter, T. S., Lightstone, F. C. & Bremer, P. T., Jan 1 2019, (Accepted/In press) In : Journal of Chemical Theory and Computation.

Research output: Contribution to journalArticle

3 Scopus citations

Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness

Sun, D., Peyear, T. A., Bennett, W. F. D., Andersen, O. S., Lightstone, F. C. & Ingólfsson, H. I., Nov 19 2019, In : Biophysical Journal. 117, 10, p. 1831-1844 14 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
2018

Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field

Carpenter, T. S., López, C. A., Neale, C., Montour, C., Ingólfsson, H. I., Di Natale, F., Lightstone, F. C. & Gnanakaran, S., Jan 1 2018, (Accepted/In press) In : Journal of Chemical Theory and Computation.

Research output: Contribution to journalArticle

17 Scopus citations

Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study

Cranford, J. P., O’Hara, T. J., Villongco, C. T., Hafez, O. M., Blake, R. C., Loscalzo, J., Fattebert, J. L., Richards, D. F., Zhang, X., Glosli, J. N., McCulloch, A. D., Krummen, D. E., Lightstone, F. C. & Wong, S. E., Sep 15 2018, In : Cardiovascular Engineering and Technology. 9, 3, p. 447-467 21 p.

Research output: Contribution to journalArticle

1 Scopus citations

Pharmacological characterization of the neurotrophic sesquiterpene jiadifenolide reveals a non-convulsant signature and potential for progression in neurodegenerative disease studies

Witkin, J. M., Shenvi, R. A., Li, X., Gleason, S. D., Weiss, J., Morrow, D., Catow, J. T., Wakulchik, M., Ohtawa, M., Lu, H. H., Martinez, M. D., Schkeryantz, J. M., Carpenter, T. S., Lightstone, F. C. & Cerne, R., Sep 1 2018, In : Biochemical Pharmacology. 155, p. 61-70 10 p.

Research output: Contribution to journalArticle

5 Scopus citations

Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase

Tang, H. Y. H., Shin, D. S., Hura, G. L., Yang, Y., Hu, X., Lightstone, F. C., McGee, M. D., Padgett, H. S., Yannone, S. M. & Tainer, J. A., Dec 4 2018, In : Biochemistry. 57, 48, p. 6688-6700 13 p.

Research output: Contribution to journalArticle

1 Scopus citations
2017

A comprehensive docking and MM/GBSA rescoring study of ligand recognition upon binding antithrombin

Zhang, X., Perez-Sanchez, H. & Lightstone, F. C., May 1 2017, In : Current Topics in Medicinal Chemistry. 17, 14, p. 1631-1639 9 p.

Research output: Contribution to journalArticle

13 Scopus citations

Computational Lipidomics of the Neuronal Plasma Membrane

Ingólfsson, H. I., Carpenter, T. S., Bhatia, H., Bremer, P. T., Marrink, S. J. & Lightstone, F. C., Nov 21 2017, In : Biophysical Journal. 113, 10, p. 2271-2280 10 p.

Research output: Contribution to journalArticle

52 Scopus citations

Predicting a Drug's Membrane Permeability: A Computational Model Validated with in Vitro Permeability Assay Data

Bennion, B., Be, N. A., McNerney, M. W., Lao, V., Carlson, E. M., Valdez, C. A., Malfatti, M. A., Enright, H. A., Nguyen, T. H., Lightstone, F. C. & Carpenter, T. S., May 25 2017, In : Journal of Physical Chemistry B. 121, 20, p. 5228-5237 10 p.

Research output: Contribution to journalArticle

47 Scopus citations

Simultaneous electrical recording of cardiac electrophysiology and contraction on chip

Qian, F., Huang, C., Lin, Y. D., Ivanovskaya, A. N., O'Hara, T. J., Booth, R. H., Creek, C. J., Enright, H. A., Soscia, D. A., Belle, A. M., Liao, R., Lightstone, F. C., Kulp, K. S. & Wheeler, E. K., Jan 1 2017, In : Lab on a Chip. 17, 10, p. 1732-1739 8 p.

Research output: Contribution to journalArticle

29 Scopus citations

The biodistribution and pharmacokinetics of the oxime acetylcholinesterase reactivator RS194B in guinea pigs

Malfatti, M. A., Enright, H. A., Be, N. A., Kuhn, E. A., Hok, S., McNerney, M. W., Lao, V., Nguyen, T. H., Lightstone, F. C., Carpenter, T. S., Bennion, B. & Valdez, C. A., Nov 1 2017, In : Chemico-Biological Interactions. 277, p. 159-167 9 p.

Research output: Contribution to journalArticle

5 Scopus citations
2016

An Electrostatic Funnel in the GABA-Binding Pathway

Carpenter, T. S. & Lightstone, F. C., Apr 1 2016, In : PLoS Computational Biology. 12, 4, e1004831.

Research output: Contribution to journalArticle

3 Scopus citations
3 Scopus citations

The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis

Yang, Y., Pan, L., Lightstone, F. C. & Merz, K. M., 2016, (Accepted/In press) In : Methods in Enzymology.

Research output: Contribution to journalArticle

3 Scopus citations
2015

A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

Bennion, B. J., Essiz, S. G., Lau, E. Y., Fattebert, J. L., Emigh, A. & Lightstone, F. C., Apr 13 2015, In : PLoS One. 10, 4, e0121092.

Research output: Contribution to journalArticle

15 Scopus citations

Carbonic anhydrase mimics for enhanced CO2 absorption in an amine-based capture solvent

Kelsey, R. A., Miller, D. A., Parkin, S. R., Liu, K., Remias, J. E., Yang, Y., Lightstone, F. C., Liu, K., Lippert, C. A. & Odom, S. A., Nov 26 2015, In : Dalton Transactions. 45, 1, p. 324-333 10 p.

Research output: Contribution to journalArticle

16 Scopus citations

Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

Fattebert, J. L., Lau, E. Y., Bennion, B. J., Huang, P. & Lightstone, F. C., Oct 22 2015, In : Journal of Chemical Theory and Computation. 11, 12, p. 5688-5695 8 p.

Research output: Contribution to journalArticle

3 Scopus citations
2014

Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines

Labute, M. X., Zhang, X., Lenderman, J., Bennion, B. J., Wong, S. E. & Lightstone, F. C., Sep 5 2014, In : PLoS One. 9, 9, e106298.

Research output: Contribution to journalArticle

38 Scopus citations

A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations

Carpenter, T. S., Kirshner, D. A., Lau, E. Y., Wong, S. E., Nilmeier, J. P. & Lightstone, F. C., Aug 5 2014, In : Biophysical Journal. 107, 3, p. 630-641 12 p.

Research output: Contribution to journalArticle

103 Scopus citations

Developing an approach for first-principles catalyst design: Application to carbon-capture catalysis

Kulik, H. J., Wong, S. E., Baker, S. E., Valdez, C. A., Satcher, J. H., Aines, R. D. & Lightstone, F. C., 2014, In : Acta Crystallographica Section C: Structural Chemistry. 70, 2, p. 123-131 9 p.

Research output: Contribution to journalArticle

9 Scopus citations

GABAa receptor target of tetramethylenedisulfotetramine

Zhao, C., Hwang, S. H., Buchholz, B. A., Carpenter, T. S., Lightstone, F. C., Yang, J., Hammock, B. D. & Casida, J. E., Jun 10 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 23, p. 8607-8612 6 p.

Research output: Contribution to journalArticle

31 Scopus citations
47 Scopus citations

Understanding a substrate's product regioselectivity in a family of enzymes: A case study of acetaminophen binding in cytochrome P450s

Yang, Y., Wong, S. E. & Lightstone, F. C., Feb 3 2014, In : PLoS One. 9, 2, e87058.

Research output: Contribution to journalArticle

19 Scopus citations
2013

Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: The use of WaterMap

Yang, Y., Lightstone, F. C. & Wong, S. E., Mar 2013, In : Expert Opinion on Drug Discovery. 8, 3, p. 277-287 11 p.

Research output: Contribution to journalArticle

33 Scopus citations

Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

Kirshner, D. A., Nilmeier, J. P. & Lightstone, F. C., Jul 2013, In : Nucleic Acids Research. 41, Web Server issue

Research output: Contribution to journalArticle

15 Scopus citations

Comparison and Analysis of Zinc and Cobalt-Based Systems as Catalytic Entities for the Hydration of Carbon Dioxide

Lau, E. Y., Wong, S. E., Baker, S. E., Bearinger, J. P., Koziol, L., Valdez, C. A., Satcher, J. H., Aines, R. D. & Lightstone, F. C., Jun 20 2013, In : PLoS One. 8, 6, e66187.

Research output: Contribution to journalArticle

9 Scopus citations

Computational analysis of a Zn-bound tris(imidazolyl) calix[6]arene aqua complex: Toward incorporating second-coordination sphere effects into carbonic anhydrase biomimetics

Koziol, L., Essiz, S. G., Wong, S. E., Lau, E. Y., Valdez, C. A., Satcher, J. H., Aines, R. D. & Lightstone, F. C., Mar 12 2013, In : Journal of Chemical Theory and Computation. 9, 3, p. 1320-1327 8 p.

Research output: Contribution to journalArticle

5 Scopus citations

Identification of a possible secondary picrotoxin-binding site on the GABAA receptor

Carpenter, T. S., Lau, E. Y. & Lightstone, F. C., 2013, In : Chemical Research in Toxicology. 26, 10, p. 1444-1454 11 p.

Research output: Contribution to journalArticle

18 Scopus citations
45 Scopus citations

Molecular recognition of aromatic rings by flavin: Electrostatics and dispersion determine ring positioning above isoalloxazine

Koziol, L., Kumar, N., Wong, S. E. & Lightstone, F. C., Dec 5 2013, In : Journal of Physical Chemistry A. 117, 48, p. 12946-12952 7 p.

Research output: Contribution to journalArticle

3 Scopus citations

Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: Development of inhibitors with broad spectrum, Gram-negative antibacterial activity

Trzoss, M., Bensen, D. C., Li, X., Chen, Z., Lam, T., Zhang, J., Creighton, C. J., Cunningham, M. L., Kwan, B., Stidham, M., Nelson, K., Brown-Driver, V., Castellano, A., Shaw, K. J., Lightstone, F. C., Wong, S. E., Nguyen, T. B., Finn, J. & Tari, L. W., Mar 1 2013, In : Bioorganic and Medicinal Chemistry Letters. 23, 5, p. 1537-1543 7 p.

Research output: Contribution to journalArticle

55 Scopus citations

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

Tari, L. W., Trzoss, M., Bensen, D. C., Li, X., Chen, Z., Lam, T., Zhang, J., Creighton, C. J., Cunningham, M. L., Kwan, B., Stidham, M., Shaw, K. J., Lightstone, F. C., Wong, S. E., Nguyen, T. B., Nix, J. & Finn, J., Mar 1 2013, In : Bioorganic and Medicinal Chemistry Letters. 23, 5, p. 1529-1536 8 p.

Research output: Contribution to journalArticle

71 Scopus citations

Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

Nilmeier, J. P., Kirshner, D. A., Wong, S. E. & Lightstone, F. C., May 10 2013, In : PLoS One. 8, 5, e62535.

Research output: Contribution to journalArticle

25 Scopus citations

Tricyclic GyrB/ParE (TriBE) inhibitors: A new class of broad-spectrum dual-targeting antibacterial agents

Tari, L. W., Li, X., Trzoss, M., Bensen, D. C., Chen, Z., Lam, T., Zhang, J., Lee, S. J., Hough, G., Phillipson, D., Akers-Rodriguez, S., Cunningham, M. L., Kwan, B. P., Nelson, K. J., Castellano, A., Locke, J. B., Brown-Driver, V., Murphy, T. M., Ong, V. S., Pillar, C. M. & 7 others, Shinabarger, D. L., Nix, J., Lightstone, F. C., Wong, S. E., Nguyen, T. B., Shaw, K. J. & Finn, J., Feb 26 2013, In : PLoS One. 8, 12, e84409.

Research output: Contribution to journalArticle

60 Scopus citations
2012

A role for loop F in modulating GABA binding affinity in the GABA A receptor

Carpenter, T. S., Lau, E. Y. & Lightstone, F. C., Sep 14 2012, In : Journal of Molecular Biology. 422, 2, p. 310-323 14 p.

Research output: Contribution to journalArticle

16 Scopus citations

Re-electrospraying splash-landed proteins and nanoparticles

Benner, W. H., Lewis, G. S., Hering, S. V., Selgelke, B., Corzett, M., Evans, J. E. & Lightstone, F. C., Mar 6 2012, In : Analytical Chemistry. 84, 5, p. 2498-2504 7 p.

Research output: Contribution to journalArticle

Toward a small molecule, biomimetic carbonic anhydrase model: Theoretical and experimental investigations of a panel of zinc(II) aza-macrocyclic catalysts

Koziol, L., Valdez, C. A., Baker, S. E., Lau, E. Y., Floyd, W. C., Wong, S. E., Satcher, J. H., Lightstone, F. C. & Aines, R. D., Jun 18 2012, In : Inorganic Chemistry. 51, 12, p. 6803-6812 10 p.

Research output: Contribution to journalArticle

57 Scopus citations
2011

Accounting for water molecules in drug design

Wong, S. E. & Lightstone, F. C., Jan 2011, In : Expert Opinion on Drug Discovery. 6, 1, p. 65-74 10 p.

Research output: Contribution to journalArticle

62 Scopus citations
2010

Halogenated benzimidazole carboxamides target integrin α 4β1 on T-cell and B-cell lymphomas

Carpenter, R. D., Natarajan, A., Lau, E. Y., Andrei, M., Solano, D. M., Lightstone, F. C., DeNardo, S. J., Lam, K. & Kurth, M. J., Jul 1 2010, In : Cancer Research. 70, 13, p. 5448-5456 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

The use of one-bead one-compound combinatorial library technology to discover high-affinity αvβ3 integrin and cancer targeting arginine-glycine-aspartic acid ligands with a built-in handle

Xiao, W., Wang, Y., Lau, E. Y., Luo, J., Yao, N., Shi, C., Meza, L., Tseng, H., Maeda, Y., Kumaresan, P., Liu, R., Lightstone, F. C., Takada, Y. & Lam, K., Oct 2010, In : Molecular Cancer Therapeutics. 9, 10, p. 2714-2723 10 p.

Research output: Contribution to journalArticle

52 Scopus citations
2009

Modeling neuronal nicotinic and GABA receptors: Important interface salt-links and protein dynamics

Law, R. J. & Lightstone, F. C., Sep 16 2009, In : Biophysical Journal. 97, 6, p. 1586-1594 9 p.

Research output: Contribution to journalArticle

20 Scopus citations

Quantitative assessment of electrostatic embedding in density functional theory calculations of biomolecular systems

Fattebert, J. L., Law, R. J., Bennion, B., Lau, E. Y., Schwegler, E. & Lightstone, F. C., Sep 2009, In : Journal of Chemical Theory and Computation. 5, 9, p. 2257-2264 8 p.

Research output: Contribution to journalArticle

6 Scopus citations

Selectively targeting T- and B-cell lymphomas: A benzothiazole antagonist of α 4β 1integrin

Carpenter, R. D., Andrei, M., Aina, O. H., Lau, E. Y., Lightstone, F. C., Liu, R., Lam, K. & Kurth, M. J., Jan 8 2009, In : Journal of Medicinal Chemistry. 52, 1, p. 14-19 6 p.

Research output: Contribution to journalArticle

27 Scopus citations
2008

An ion gating mechanism of gastric H,K-ATPase based on molecular dynamics simulations

Law, R. J., Munson, K., Sachs, G. & Lightstone, F. C., Sep 15 2008, In : Biophysical Journal. 95, 6, p. 2739-2749 11 p.

Research output: Contribution to journalArticle

12 Scopus citations

First principles and classical molecular dynamics simulations of solvated benzene

Allesch, M., Lightstone, F. C., Schwegler, E. & Galli, G., 2008, In : Journal of Chemical Physics. 128, 1, 014501.

Research output: Contribution to journalArticle

28 Scopus citations