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ArticlesPeer ReviewedFull Text
Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines
Author / Creator:LaBute, Montiago X ; Zhang, Xiaohua ; Lenderman, Jason ; Bennion, Brian J ; Wong, Sergio E ; Lightstone, Felice C
Publisher:United States: Public Library of Science
Journal title:PloS one, 2014-09, Vol.9 (9), p.e106298
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OFraMP: a fragment-based tool to facilitate the parametrization of large molecules
Author / Creator:Stroet, Martin ; Caron, Bertrand ; Engler, Martin S. ; van der Woning, Jimi ; Kauffmann, Aude ; van Dijk, Marc ; El-Kebir, Mohammed ; Visscher, Koen M. ; Holownia, Josef ; Macfarlane, Callum ; Bennion, Brian J. ; Gelpi-Dominguez, Svetlana ; Lightstone, Felice C. ; van der Storm, Tijs ; Geerke, Daan P. ; Mark, Alan E. ; Klau, Gunnar W.
Publisher:Cham: Springer International Publishing
Journal title:Journal of computer-aided molecular design, 2023-08, Vol.37 (8), p.357-371
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Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach
Author / Creator:Bennion, Brian J. ; Malfatti, Michael A. ; Be, Nicholas A. ; Enright, Heather A. ; Hok, Saphon ; Cadieux, C. Linn ; Carpenter, Timothy S. ; Lao, Victoria ; Kuhn, Edward A. ; McNerney, M. Windy ; Lightstone, Felice C. ; Nguyen, Tuan H. ; Valdez, Carlos A.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2021-07, Vol.11 (1), p.15567-16, Article 15567
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Understanding a substrate's product regioselectivity in a family of enzymes: a case study of acetaminophen binding in cytochrome P450s
Author / Creator:Yang, Yue ; Wong, Sergio E ; Lightstone, Felice C
Publisher:United States: Public Library of Science
Journal title:PloS one, 2014-02, Vol.9 (2), p.e87058-e87058
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Newsletter articlesFull Text
WIPO PUBLISHES PATENT OF LAWRENCE LIVERMORE NATIONAL SECURITY, VALDEZ CARLOS A., SATCHER JR. JOE H., AINES ROGER D., WONG SERGIO E., BAKER SARAH E., LIGHTSTONE FELICE C., STOLAROFF JOSHUAH K. FOR "TET...
Publisher:Washington, D.C: HT Digital Streams Limited
Journal title:US Fed News Service, Including US State News, 2012
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A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations
Author / Creator:Bennion, Brian J ; Essiz, Sebnem G ; Lau, Edmond Y ; Fattebert, Jean-Luc ; Emigh, Aiyana ; Lightstone, Felice C
Publisher:United States: Public Library of Science
Journal title:PloS one, 2015-04, Vol.10 (4), p.e0121092-e0121092
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An Electrostatic Funnel in the GABA-Binding Pathway
Author / Creator:Carpenter, Timothy S ; Lightstone, Felice C
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2016-04, Vol.12 (4), p.e1004831-e1004831
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Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior
Author / Creator:Goswami, Debanjan ; Chen, De ; Yang, Yue ; Gudla, Prabhakar R ; Columbus, John ; Worthy, Karen ; Rigby, Megan ; Wheeler, Madeline ; Mukhopadhyay, Suman ; Powell, Katie ; Burgan, William ; Wall, Vanessa ; Esposito, Dominic ; Simanshu, Dhirendra K ; Lightstone, Felice C ; Nissley, Dwight V ; McCormick, Frank ; Turbyville, Thomas
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2020-01, Vol.9
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Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane
Author / Creator:Shrestha, Rebika ; Carpenter, Timothy S. ; Van, Que N. ; Agamasu, Constance ; Tonelli, Marco ; Aydin, Fikret ; Chen, De ; Gulten, Gulcin ; Glosli, James N. ; López, Cesar A. ; Oppelstrup, Tomas ; Neale, Chris ; Gnanakaran, Sandrasegaram ; Gillette, William K. ; Ingólfsson, Helgi I. ; Lightstone, Felice C. ; Stephen, Andrew G. ; Streitz, Frederick H. ; Nissley, Dwight V. ; Turbyville, Thomas J.
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2024-02, Vol.7 (1), p.242-16, Article 242
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ArticlesPeer ReviewedFull Text
Rapid catalytic template searching as an enzyme function prediction procedure
Author / Creator:Nilmeier, Jerome P ; Kirshner, Daniel A ; Wong, Sergio E ; Lightstone, Felice C
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-05, Vol.8 (5), p.e62535-e62535
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ArticlesPeer ReviewedFull Text
Author Correction: Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane
Author / Creator:Shrestha, Rebika ; Carpenter, Timothy S. ; Van, Que N. ; Agamasu, Constance ; Tonelli, Marco ; Aydin, Fikret ; Chen, De ; Gulten, Gulcin ; Glosli, James N. ; López, Cesar A. ; Oppelstrup, Tomas ; Neale, Chris ; Gnanakaran, Sandrasegaram ; Gillette, William K. ; Ingólfsson, Helgi I. ; Lightstone, Felice C. ; Stephen, Andrew G. ; Streitz, Frederick H. ; Nissley, Dwight V. ; Turbyville, Thomas J.
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2024-04, Vol.7 (1), p.445-1, Article 445
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ArticlesPeer ReviewedFull Text
Comprehensive characterization of protein–protein interactions perturbed by disease mutations
Author / Creator:Cheng, Feixiong ; Zhao, Junfei ; Wang, Yang ; Lu, Weiqiang ; Liu, Zehui ; Zhou, Yadi ; Martin, William R. ; Wang, Ruisheng ; Huang, Jin ; Hao, Tong ; Yue, Hong ; Ma, Jing ; Hou, Yuan ; Castrillon, Jessica A. ; Fang, Jiansong ; Lathia, Justin D. ; Keri, Ruth A. ; Lightstone, Felice C. ; Antman, Elliott Marshall ; Rabadan, Raul ; Hill, David E. ; Eng, Charis ; Vidal, Marc ; Loscalzo, Joseph
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2021-03, Vol.53 (3), p.342-353
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ArticlesPeer ReviewedFull Text
Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide
Author / Creator:Lau, Edmond Y ; Wong, Sergio E ; Baker, Sarah E ; Bearinger, Jane P ; Koziol, Lucas ; Valdez, Carlos A ; Satcher, Jr, Joseph H ; Aines, Roger D ; Lightstone, Felice C
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-06, Vol.8 (6), p.e66187-e66187
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ArticlesPeer ReviewedFull Text
In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR complex
Author / Creator:Martin, William R ; Lightstone, Felice C ; Cheng, Feixiong
Publisher:Switzerland: MDPI
Journal title:International journal of molecular sciences, 2020-02, Vol.21 (5), p.1550
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ArticlesPeer ReviewedFull Text
An Ion Gating Mechanism of Gastric H,K-ATPase Based on Molecular Dynamics Simulations
Author / Creator:Law, Richard J. ; Munson, Keith ; Sachs, George ; Lightstone, Felice C.
Publisher:United States: Elsevier Inc
Journal title:Biophysical journal, 2008-09, Vol.95 (6), p.2739-2749
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ArticlesPeer ReviewedFull Text
Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
Author / Creator:Ingólfsson, Helgi I. ; Neale, Chris ; Carpenter, Timothy S. ; Shrestha, Rebika ; López, Cesar A. ; Tran, Timothy H. ; Oppelstrup, Tomas ; Bhatia, Harsh ; Stanton, Liam G. ; Zhang, Xiaohua ; Sundram, Shiv ; Di Natale, Francesco ; Agarwal, Animesh ; Dharuman, Gautham ; Schumacher, Sara I. L. Kokkila ; Turbyville, Thomas ; Gulten, Gulcin ; Van, Que N. ; Goswami, Debanjan ; Jean-Francois, Frantz ; Agamasu, Constance ; Chen, De ; Hettige, Jeevapani J. ; Travers, Timothy ; Sarkar, Sumantra ; Surh, Michael P. ; Yang, Yue ; Moody, Adam ; Liu, Shusen ; Van Essen, Brian C. ; Voter, Arthur F. ; Ramanathan, Arvind ; Hengartner, Nicolas W. ; Simanshu, Dhirendra K. ; Stephen, Andrew G. ; Bremer, Peer-Timo ; Gnanakaran, S. ; Glosli, James N. ; Lightstone, Felice C. ; McCormick, Frank ; Nissley, Dwight V. ; Streitz, Frederick H.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2022-01, Vol.119 (1), p.1-10
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ArticlesPeer ReviewedFull Text
PDBspheres: a method for finding 3D similarities in local regions in proteins
Author / Creator:Zemla, Adam T ; Allen, Jonathan E ; Kirshner, Dan ; Lightstone, Felice C
Publisher:Oxford: Oxford University Press
Journal title:NAR genomics and bioinformatics, 2022-12, Vol.4 (4), p.lqac078-lqac078
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ArticlesPeer ReviewedFull Text
Tricyclic GyrB/ParE (TriBE) inhibitors: a new class of broad-spectrum dual-targeting antibacterial agents
Author / Creator:Tari, Leslie W ; Li, Xiaoming ; Trzoss, Michael ; Bensen, Daniel C ; Chen, Zhiyong ; Lam, Thanh ; Zhang, Junhu ; Lee, Suk Joong ; Hough, Grayson ; Phillipson, Doug ; Akers-Rodriguez, Suzanne ; Cunningham, Mark L ; Kwan, Bryan P ; Nelson, Kirk J ; Castellano, Amanda ; Locke, Jeff B ; Brown-Driver, Vickie ; Murphy, Timothy M ; Ong, Voon S ; Pillar, Chris M ; Shinabarger, Dean L ; Nix, Jay ; Lightstone, Felice C ; Wong, Sergio E ; Nguyen, Toan B ; Shaw, Karen J ; Finn, John
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-12, Vol.8 (12), p.e84409-e84409
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ArticlesPeer ReviewedFull Text
Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations
Author / Creator:Bhatia, Harsh ; Carpenter, Timothy S. ; Ingólfsson, Helgi I. ; Dharuman, Gautham ; Karande, Piyush ; Liu, Shusen ; Oppelstrup, Tomas ; Neale, Chris ; Lightstone, Felice C. ; Van Essen, Brian ; Glosli, James N. ; Bremer, Peer-Timo
Publisher:London: Nature Publishing Group UK
Journal title:Nature machine intelligence, 2021-05, Vol.3 (5), p.401-409
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ArticlesPeer ReviewedFull Text
Mass spectrometry and non-covalent protein-ligand complexes: confirmation of binding sites and changes in tertiary structure
Author / Creator:Shields, Sharon J ; Oyeyemi, Olayinka ; Lightstone, Felice C ; Balhorn, Rod
Publisher:New York, NY: Elsevier Inc
Journal title:Journal of the American Society for Mass Spectrometry, 2003-05, Vol.14 (5), p.460-470
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Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines

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OFraMP: a fragment-based tool to facilitate the parametrization of large molecules

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Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach

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

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WIPO PUBLISHES PATENT OF LAWRENCE LIVERMORE NATIONAL SECURITY, VALDEZ CARLOS A., SATCHER JR. JOE H., AINES ROGER D., WONG SERGIO E., BAKER SARAH E., LIGHTSTONE FELICE C., STOLAROFF JOSHUAH K. FOR "TET...

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

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An Electrostatic Funnel in the GABA-Binding Pathway

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

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Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

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Rapid catalytic template searching as an enzyme function prediction procedure

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Author Correction: Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

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Comprehensive characterization of protein–protein interactions perturbed by disease mutations

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Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide

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In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR complex

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An Ion Gating Mechanism of Gastric H,K-ATPase Based on Molecular Dynamics Simulations

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Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins

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PDBspheres: a method for finding 3D similarities in local regions in proteins

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

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Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations

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Mass spectrometry and non-covalent protein-ligand complexes: confirmation of binding sites and changes in tertiary structure

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