Search Results - "Lightstone, Felice C"

A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin by Zhang, Xiaohua, Perez-Sanchez, Horacio, Lightstone, Felice C

“…A high-throughput virtual screening pipeline has been extended from single energetically minimized structure Molecular Mechanics/Generalized Born Surface Area…”
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Computational Lipidomics of the Neuronal Plasma Membrane by Ingólfsson, Helgi I., Carpenter, Timothy S., Bhatia, Harsh, Bremer, Peer-Timo, Marrink, Siewert J., Lightstone, Felice C.

“…Membrane lipid composition varies greatly within submembrane compartments, different organelle membranes, and also between cells of different cell stage, cell…”
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A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations by Carpenter, Timothy S., Kirshner, Daniel A., Lau, Edmond Y., Wong, Sergio E., Nilmeier, Jerome P., Lightstone, Felice C.

“…The blood-brain barrier (BBB) is formed by specialized tight junctions between endothelial cells that line brain capillaries to create a highly selective…”
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Simultaneous electrical recording of cardiac electrophysiology and contraction on chip by Qian, Fang, Huang, Chao, Lin, Yi-Dong, Ivanovskaya, Anna N, O'Hara, Thomas J, Booth, Ross H, Creek, Cameron J, Enright, Heather A, Soscia, David A, Belle, Anna M, Liao, Ronglih, Lightstone, Felice C, Kulp, Kristen S, Wheeler, Elizabeth K

“…Prevailing commercialized cardiac platforms for in vitro drug development utilize planar microelectrode arrays to map action potentials, or impedance sensing…”
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Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines by LaBute, Montiago X, Zhang, Xiaohua, Lenderman, Jason, Bennion, Brian J, Wong, Sergio E, Lightstone, Felice C

“…Late-stage or post-market identification of adverse drug reactions (ADRs) is a significant public health issue and a source of major economic liability for…”
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In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR complex by Martin, William R, Lightstone, Felice C, Cheng, Feixiong

“…Gain-of-function mutations in PCSK9 (proprotein convertase subtilisin/kexin type 9) lead to reduced uptake of LDL (low density lipoprotein) cholesterol and,…”
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Atomistic Characterization of Gramicidin Channel Formation by Sun, Delin, He, Stewart, Bennett, W. F. Drew, Bilodeau, Camille L, Andersen, Olaf S, Lightstone, Felice C, Ingólfsson, Helgi I

“…We investigated gramicidin A (gA) subunit dimerization in lipid bilayers using microsecond-long replica-exchange umbrella sampling simulations,…”
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OFraMP: a fragment-based tool to facilitate the parametrization of large molecules by 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.

“…An Online tool for Fragment-based Molecule Parametrization (OFraMP) is described. OFraMP is a web application for assigning atomic interaction parameters to…”
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Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach by 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.

“…Nerve agents have experienced a resurgence in recent times with their use against civilian targets during the attacks in Syria (2012), the poisoning of Sergei…”
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Understanding a substrate's product regioselectivity in a family of enzymes: a case study of acetaminophen binding in cytochrome P450s by Yang, Yue, Wong, Sergio E, Lightstone, Felice C

“…Product regioselectivity as influenced by molecular recognition is a key aspect of enzyme catalysis. We applied large-scale two-dimensional (2D) umbrella…”
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A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations by Bennion, Brian J, Essiz, Sebnem G, Lau, Edmond Y, Fattebert, Jean-Luc, Emigh, Aiyana, Lightstone, Felice C

“…Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and…”
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An Electrostatic Funnel in the GABA-Binding Pathway by Carpenter, Timothy S, Lightstone, Felice C

“…The γ-aminobutyric acid type A receptor (GABAA-R) is a major inhibitory neuroreceptor that is activated by the binding of GABA. The structure of the GABAA-R is…”
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Pharmacological characterization of the neurotrophic sesquiterpene jiadifenolide reveals a non-convulsant signature and potential for progression in neurodegenerative disease studies by Witkin, Jeffrey M., Shenvi, Ryan A., Li, Xia, Gleason, Scott D., Weiss, Julie, Morrow, Denise, Catow, John T., Wakulchik, Mark, Ohtawa, Masaki, Lu, Hai-Hua, Martinez, Michael D., Schkeryantz, Jeffrey M., Carpenter, Timothy S., Lightstone, Felice C., Cerne, Rok

“…[Display omitted] The ‘neurotrophic sesquiterpenes’ refer to a group of molecules derived from the Illicium genus of flowering plant. They display neurotrophic…”
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Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior by 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

“…The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma…”
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Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB by Kirshner, Daniel A, Nilmeier, Jerome P, Lightstone, Felice C

“…The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein…”
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Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap by Yang, Yue, Lightstone, Felice C, Wong, Sergio E

“…Water displacement plays critical role in several phases of drug discovery. Proper treatment of displacing water could improve enrichment in virtual screening…”
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Rapid catalytic template searching as an enzyme function prediction procedure by Nilmeier, Jerome P, Kirshner, Daniel A, Wong, Sergio E, Lightstone, Felice C

“…We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The…”
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Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction by Fan, Ya Ju, Allen, Jonathan E., McLoughlin, Kevin S., Shi, Da, Bennion, Brian J., Zhang, Xiaohua, Lightstone, Felice C.

“…Neural Network (NN) models provide potential to speed up the drug discovery process and reduce its failure rates. The success of NN models requires uncertainty…”
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Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane by 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.

“…The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due…”
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Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline by Lau, Edmond Y., Negrete, Oscar A., Bennett, W. F. Drew, Bennion, Brian J., Borucki, Monica, Bourguet, Feliza, Epstein, Aidan, Franco, Magdalena, Harmon, Brooke, He, Stewart, Jones, Derek, Kim, Hyojin, Kirshner, Daniel, Lao, Victoria, Lo, Jacky, McLoughlin, Kevin, Mosesso, Richard, Murugesh, Deepa K., Saada, Edwin A., Segelke, Brent, Stefan, Maxwell A., Stevenson, Garrett A., Torres, Marisa W., Weilhammer, Dina R., Wong, Sergio, Yang, Yue, Zemla, Adam, Zhang, Xiaohua, Zhu, Fangqiang, Allen, Jonathan E., Lightstone, Felice C.

“…A rapid response is necessary to contain emergent biological outbreaks before they can become pandemics. The novel coronavirus (SARS-CoV-2) that causes…”
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