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Felice C. Lightstone - Publications

Affiliations: 
Lawrence Livermore National Laboratory, Livermore, CA, United States 
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29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Stevenson GA, Kirshner D, Bennion BJ, Yang Y, Zhang X, Zemla A, Torres MW, Epstein A, Jones D, Kim H, Bennett WFD, Wong SE, Allen JE, Lightstone FC. Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. Journal of Chemical Information and Modeling. PMID 37847557 DOI: 10.1021/acs.jcim.3c00722  0.341
2023 Fan YJ, Allen JE, McLoughlin KS, Shi D, Bennion BJ, Zhang X, Lightstone FC. Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction. Artificial Intelligence Chemistry. 1. PMID 37583465 DOI: 10.1016/j.aichem.2023.100004  0.33
2023 Ingólfsson HI, Bhatia H, Aydin F, Oppelstrup T, López CA, Stanton LG, Carpenter TS, Wong S, Di Natale F, Zhang X, Moon JY, Stanley CB, Chavez JR, Nguyen K, Dharuman G, ... ... Lightstone FC, et al. Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure. Journal of Chemical Theory and Computation. PMID 37075065 DOI: 10.1021/acs.jctc.2c01018  0.346
2022 López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, ... ... Lightstone FC, et al. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. Journal of Chemical Theory and Computation. PMID 35866871 DOI: 10.1021/acs.jctc.2c00168  0.369
2022 Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, ... ... Lightstone FC, et al. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophysical Journal. PMID 35778842 DOI: 10.1016/j.bpj.2022.06.035  0.344
2022 Ingólfsson HI, Neale C, Carpenter TS, Shrestha R, López CA, Tran TH, Oppelstrup T, Bhatia H, Stanton LG, Zhang X, Sundram S, Di Natale F, Agarwal A, Dharuman G, Kokkila Schumacher SIL, ... ... Lightstone FC, et al. Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 34983849 DOI: 10.1073/pnas.2113297119  0.331
2021 Lau EY, Negrete OA, Bennett WFD, Bennion BJ, Borucki M, Bourguet F, Epstein A, Franco M, Harmon B, He S, Jones D, Kim H, Kirshner D, Lao V, Lo J, ... ... Lightstone FC, et al. Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline. Frontiers in Molecular Biosciences. 8: 678701. PMID 34327214 DOI: 10.3389/fmolb.2021.678701  0.316
2021 Jones D, Kim H, Zhang X, Zemla A, Stevenson G, Bennett WFD, Kirshner D, Wong SE, Lightstone FC, Allen JE. Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. Journal of Chemical Information and Modeling. PMID 33754707 DOI: 10.1021/acs.jcim.0c01306  0.374
2020 Ingólfsson HI, Bhatia H, Zeppelin T, Bennett WFD, Carpenter KA, Hsu PC, Dharuman G, Bremer PT, Schiøtt B, Lightstone FC, Carpenter TS. Capturing biologically complex tissue-specific membranes at different levels of compositional complexity. The Journal of Physical Chemistry. B. PMID 32790367 DOI: 10.1021/Acs.Jpcb.0C03368  0.498
2020 Zhang X, Sundram S, Oppelstrup T, Kokkila-Schumacher SIL, Carpenter TS, Ingólfsson HI, Streitz FH, Lightstone FC, Glosli JN. ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. The Journal of Chemical Physics. 153: 045103. PMID 32752727 DOI: 10.1063/5.0014500  0.31
2020 Zhu F, Zhang X, Allen J, Jones D, Lightstone FC. Binding Affinity Prediction by Pairwise Function Based on Neural Network. Journal of Chemical Information and Modeling. PMID 32338892 DOI: 10.1021/acs.jcim.0c00026  0.362
2018 Cranford JP, O'Hara TJ, Villongco CT, Hafez OM, Blake RC, Loscalzo J, Fattebert JL, Richards DF, Zhang X, Glosli JN, McCulloch AD, Krummen DE, Lightstone FC, Wong SE. Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study. Cardiovascular Engineering and Technology. PMID 29549620 DOI: 10.1007/S13239-018-0347-0  0.328
2016 Zhang X, Perez-Sanchez H, Lightstone FC. A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin. Current Topics in Medicinal Chemistry. PMID 27852201  0.367
2014 LaBute MX, Zhang X, Lenderman J, Bennion BJ, Wong SE, Lightstone FC. Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines. Plos One. 9: e106298. PMID 25191698 DOI: 10.1371/Journal.Pone.0106298  0.323
2014 Kulik HJ, Wong SE, Baker SE, Valdez CA, Satcher JH, Aines RD, Lightstone FC. Developing an approach for first-principles catalyst design: application to carbon-capture catalysis. Acta Crystallographica. Section C, Structural Chemistry. 70: 123-31. PMID 24508957 DOI: 10.1107/S2053229613027666  0.538
2014 Zhang X, Wong SE, Lightstone FC. 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. Journal of Chemical Information and Modeling. 54: 324-37. PMID 24358939 DOI: 10.1021/ci4005145  0.355
2013 Zhang X, Wong SE, Lightstone FC. Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines. Journal of Computational Chemistry. 34: 915-27. PMID 23345155 DOI: 10.1002/jcc.23214  0.317
2011 Satcher JH, Baker SE, Kulik HJ, Valdez CA, Krueger RL, Lightstone FC, Aines RD. Modeling, synthesis and characterization of zinc containing carbonic anhydrase active site mimics Energy Procedia. 4: 2090-2095. DOI: 10.1016/J.Egypro.2011.02.092  0.503
2011 Wong SE, Lau EY, Kulik HJ, Satcher JH, Valdez C, Worsely M, Lightstone FC, Aines R. Designing small-molecule catalysts for CO2 capture Energy Procedia. 4: 817-823. DOI: 10.1016/J.Egypro.2011.01.124  0.538
1999 Bruice TC, Lightstone FC. Ground state and transition state contributions to the rates of intramolecular and enzymatic reactions Accounts of Chemical Research. 32: 127-136. DOI: 10.1021/Ar960131Y  0.404
1998 Lightstone FC, Zheng YJ, Bruice TC. Molecular dynamics simulations of ground and transition states for the S(N)2 displacement of Cl- from 1,2-dichloroethane at the active site of Xanthobacter autotrophicus haloalkane dehalogenase Journal of the American Chemical Society. 120: 5611-5621. DOI: 10.1021/Ja980162J  0.398
1998 Lightstone FC, Bruice TC. Enthalpy and entropy in ring closure reactions Bioorganic Chemistry. 26: 193-199. DOI: 10.1006/Bioo.1998.1096  0.342
1998 Lightstone FC, Zheng YJ, Bruice TC. The structures of the enzyme-substrate complex and transition state formed in the S(N)2 displacement of Cl- from 1,2-dichloroethane at the active site of Xanthobacter autotrophicus haloalkane dehalogenase Bioorganic Chemistry. 26: 169-174. DOI: 10.1006/Bioo.1998.1093  0.378
1997 Lightstone FC, Zheng YJ, Maulitz AH, Bruice TC. Non-enzymatic and enzymatic hydrolysis of alkyl halides: a haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction. Proceedings of the National Academy of Sciences of the United States of America. 94: 8417-20. PMID 9237991 DOI: 10.1073/Pnas.94.16.8417  0.437
1997 Maulitz AH, Lightstone FC, Zheng YJ, Bruice TC. Nonenzymatic and enzymatic hydrolysis of alkyl halides: a theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides. Proceedings of the National Academy of Sciences of the United States of America. 94: 6591-5. PMID 9192609 DOI: 10.1073/Pnas.94.13.6591  0.399
1997 Lightstone FC, Bruice TC. Separation of ground state and transition state effects in intramolecular and enzymatic reactions. 2. A theoretical study of the formation of transition states in cyclic anhydride formation Journal of the American Chemical Society. 119: 9103-9113. DOI: 10.1021/Ja970982G  0.401
1997 Bruice TC, Yip YC, Blaskó A, Lightstone FC, Browne KA, Petyak ME, Luo J. Design, synthesis, and characterization of a novel hexa-azacyclophane and interactions with d(CGCA3T3GCG)2, ctDNA and T4DNA Tetrahedron. 53: 8105-8120. DOI: 10.1016/S0040-4020(97)00501-2  0.61
1996 Lightstone FC, Bruice TC. Ground state conformations and entropic and enthalpic factors in the efficiency of intramolecular and enzymatic reactions. 1. Cyclic anhydride formation by substituted glutarates, succinate, and 3,6-endoxo-Δ4-tetrahydrophthalate monophenyl esters Journal of the American Chemical Society. 118: 2595-2605. DOI: 10.1021/Ja952589L  0.42
1994 Lightstone FC, Bruice TC. Geminal-dialkyl substitution, intramolecular reactions, and enzyme efficiency Journal of the American Chemical Society. 116: 10789-10790. DOI: 10.1021/Ja00102A056  0.347
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