Search Results - "Duca, S"

Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening by Chen, Lieyang, Cruz, Anthony, Ramsey, Steven, Dickson, Callum J, Duca, Jose S, Hornak, Viktor, Koes, David R, Kurtzman, Tom

“…Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to…”
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Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments by Lamprakis, Christos, Andreadelis, Ioannis, Manchester, John, Velez-Vega, Camilo, Duca, José S, Cournia, Zoe

“…Protein–protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would…”
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Rethinking drug design in the artificial intelligence era by Schneider, Petra, Walters, W. Patrick, Plowright, Alleyn T., Sieroka, Norman, Listgarten, Jennifer, Goodnow, Robert A., Fisher, Jasmin, Jansen, Johanna M., Duca, José S., Rush, Thomas S., Zentgraf, Matthias, Hill, John Edward, Krutoholow, Elizabeth, Kohler, Matthias, Blaney, Jeff, Funatsu, Kimito, Luebkemann, Chris, Schneider, Gisbert

“…Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some protagonists point to vast opportunities potentially offered by…”
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Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling by Dickson, Callum J, Hornak, Viktor, Pearlstein, Robert A, Duca, Jose S

“…Passive membrane permeation of small molecules is essential to achieve the required absorption, distribution, metabolism, and excretion (ADME) profiles of drug…”
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Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K‑Ras4B Dimer Stability by Andreadelis, Ioannis, Kiriakidi, Sofia, Lamprakis, Christos, Theodoropoulou, Anastasia, Doerr, Stefan, Chatzigoulas, Alexios, Manchester, John, Velez-Vega, Camilo, Duca, José S, Cournia, Zoe

“…Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can…”
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Revealing Molecular Determinants of hERG Blocker and Activator Binding by Dickson, Callum J, Velez-Vega, Camilo, Duca, Jose S

“…The Kv11.1 potassium channel, encoded by the human ether-a-go-go-related gene (hERG), plays an essential role in the cardiac action potential. hERG blockade by…”
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Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease by Pavlova, Anna, Lynch, Diane L, Daidone, Isabella, Zanetti-Polzi, Laura, Smith, Micholas Dean, Chipot, Chris, Kneller, Daniel W, Kovalevsky, Andrey, Coates, Leighton, Golosov, Andrei A, Dickson, Callum J, Velez-Vega, Camilo, Duca, José S, Vermaas, Josh V, Pang, Yui Tik, Acharya, Atanu, Parks, Jerry M, Smith, Jeremy C, Gumbart, James C

“…The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many…”
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Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations by Velez-Vega, Camilo, McKay, Daniel J. J, Kurtzman, Tom, Aravamuthan, Vibhas, Pearlstein, Robert A, Duca, José S

“…A statistical-mechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of…”
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Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications by Koukos, Panagiotis I., Dehghani-Ghahnaviyeh, Sepehr, Velez-Vega, Camilo, Manchester, John, Tieleman, D. Peter, Duca, José S., Souza, Paulo C. T., Cournia, Zoe

“…Protein lipidations are vital co/post-translational modifications that tether lipid tails to specific protein amino acids, allowing them to anchor to…”
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Chronic heat stress affects the photosynthetic apparatus of Solanum lycopersicum L. cv Micro-Tom by Parrotta, L., Aloisi, I., Faleri, C., Romi, M., Del Duca, S., Cai, G.

“…Tomato (Solanum lycopersicum L.) is one of the most widely cultivated crops in the world. Tomato is a plant model and the relationship between yield and…”
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Arabidopsis SHR and SCR transcription factors and AUX1 auxin influx carrier control the switch between adventitious rooting and xylogenesis in planta and in in vitro cultured thin cell layers by Della Rovere, F., Fattorini, L., D’Angeli, S., Veloccia, A., Del Duca, S., Cai, G., Falasca, G., Altamura, M. M.

“…Adventitious roots (ARs) are essential for vegetative propagation. The Arabidopsis thaliana transcription factors SHORT ROOT (SHR) and SCARECROW (SCR) affect…”
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A permafrost test on intact gneiss rock by Duca, S., Alonso, E.E., Scavia, C.

“…Changes in permafrost conditions in high mountain rocks have increased the risk of dangerous instabilities. Ice segregation within the rock mass has been…”
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Transglutaminase as polyamine mediator in plant growth and differentiation by Aloisi, I., Cai, G., Serafini-Fracassini, D., Del Duca, S.

“…Transglutaminases (TGases) are ubiquitous enzymes catalyzing many biological reactions. The best-known TGase activity, namely the transamidation of specific…”
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Polyamines are common players in different facets of plant programmed cell death by Cai, G, Sobieszczuk-Nowicka, E, Aloisi, I, Fattorini, L, Serafini-Fracassini, D, Del Duca, S

“…Programmed cell death (PCD) is a process that occurs throughout the life span of every plant life, from initial germination of the seed to the senescence of…”
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AtPng1 knockout mutant of Arabidopsis thaliana shows a juvenile phenotype, morpho-functional changes, altered stress response and cell wall modifications by Serafini-Fracassini, D., Della Mea, M., Parrotta, L., Faleri, C., Cai, G., Del Duca, S., Aloisi, I.

“…In order to ascertain the role of plant transglutaminases (TGase) in growth and abiotic stress response, the AtPng1 knock out (KO) line of A. thaliana has been…”
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Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation by Pearlstein, Robert A, MacCannell, K Andrew, Erdemli, Gül, Yeola, Sarita, Helmlinger, Gabriel, Hu, Qi-Ying, Farid, Ramy, Egan, William, Whitebread, Steven, Springer, Clayton, Beck, Jeremy, Wang, Hao-Ran, Maciejewski, Mateusz, Urban, Laszlo, Duca, José S

“…Blockade of the hERG potassium channel prolongs the ventricular action potential (AP) and QT interval, and triggers early after depolarizations (EADs) and…”
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Gray matter reduction in high-risk subjects, recently diagnosed and chronic patients with schizophrenia: A revised coordinate-based meta-analysis by Brasso, C., Liloia, D., Cauda, F., Mancuso, L., Nani, A., Manuello, J., Costa, T., Duca, S., Rocca, P.

“…Introduction Characterizing neuroanatomical markers of different stages of schizophrenia (SZ) to assess of how the disorder develops is extremely important for…”
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Determination of Transglutaminase Activity in Plants by Del Duca, S, Bonner, P L R, Aloisi, I, Serafini-Fracassini, D, Cai, G

“…Transglutaminase (TGase:E.C. 2.3.2.13) catalyzes the acyl-transfer reaction between one or two primary amino groups of polyamines and protein-bound Gln…”
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Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH by Velez-Vega, Camilo, McKay, Daniel J. J, Aravamuthan, Vibhas, Pearlstein, Robert, Duca, José S

“…Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were…”
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Dark-induced senescence of barley leaves involves activation of plastid transglutaminases by Sobieszczuk-Nowicka, E., Zmienko, A., Samelak-Czajka, A., Łuczak, M., Pietrowska-Borek, M., Iorio, R., Del Duca, S., Figlerowicz, M., Legocka, J.

“…Transglutaminases (E.C. 2.3.2.13) catalyze the post-translational modification of proteins by establishing ε-(γ-glutamyl) lysine isopeptide bonds and by the…”
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