Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments
Lamprakis, Christos, Andreadelis, Ioannis, Manchester, John, Velez-Vega, Camilo, Duca, José S, Cournia, Zoe
Published in Journal of chemical theory and computation (11.05.2021)
Published in Journal of chemical theory and computation (11.05.2021)
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PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks
Jiménez, José, Sabbadin, Davide, Cuzzolin, Alberto, Martínez-Rosell, Gerard, Gora, Jacob, Manchester, John, Duca, José, De Fabritiis, Gianni
Published in Journal of chemical information and modeling (25.03.2019)
Published in Journal of chemical information and modeling (25.03.2019)
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Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2
Ahmed, Syed Sohail, Volkmuth, Wayne, Duca, José, Corti, Lorenzo, Pallaoro, Michele, Pezzicoli, Alfredo, Karle, Anette, Rigat, Fabio, Rappuoli, Rino, Narasimhan, Vas, Julkunen, Ilkka, Vuorela, Arja, Vaarala, Outi, Nohynek, Hanna, Pasini, Franco Laghi, Montomoli, Emanuele, Trombetta, Claudia, Adams, Christopher M, Rothbard, Jonathan, Steinman, Lawrence
Published in Science translational medicine (01.07.2015)
Published in Science translational medicine (01.07.2015)
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Synthesis of New 4,5-Dihydrofuranoindoles and Their Evaluation as HCV NS5B Polymerase Inhibitors
Velázquez, Francisco, Venkatraman, Srikanth, Lesburg, Charles A, Duca, José, Rosenblum, Stuart B, Kozlowski, Joseph A, Njoroge, F. George
Published in Organic letters (20.01.2012)
Published in Organic letters (20.01.2012)
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Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology
Pearlstein, Robert A, McKay, Daniel J J, Hornak, Viktor, Dickson, Callum, Golosov, Andrei, Harrison, Tyler, Velez-Vega, Camilo, Duca, José
Published in Current topics in medicinal chemistry (01.01.2017)
Published in Current topics in medicinal chemistry (01.01.2017)
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Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening
Chen, Lieyang, Cruz, Anthony, Ramsey, Steven, Dickson, Callum J, Duca, Jose S, Hornak, Viktor, Koes, David R, Kurtzman, Tom
Published in PloS one (20.08.2019)
Published in PloS one (20.08.2019)
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Rethinking drug design in the artificial intelligence era
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
Published in Nature reviews. Drug discovery (01.05.2020)
Published in Nature reviews. Drug discovery (01.05.2020)
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Cross-Docking of Inhibitors into CDK2 Structures. 1
Duca, José S, Madison, Vincent S, Voigt, Johannes H
Published in Journal of chemical information and modeling (01.03.2008)
Published in Journal of chemical information and modeling (01.03.2008)
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Journal Article
Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications
Koukos, Panagiotis I., Dehghani-Ghahnaviyeh, Sepehr, Velez-Vega, Camilo, Manchester, John, Tieleman, D. Peter, Duca, José S., Souza, Paulo C. T., Cournia, Zoe
Published in Journal of chemical theory and computation (12.12.2023)
Published in Journal of chemical theory and computation (12.12.2023)
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Cross-Docking of Inhibitors into CDK2 Structures. 2
Voigt, Johannes H, Elkin, Carl, Madison, Vincent S, Duca, José S
Published in Journal of chemical information and modeling (01.03.2008)
Published in Journal of chemical information and modeling (01.03.2008)
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Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K‑Ras4B Dimer Stability
Andreadelis, Ioannis, Kiriakidi, Sofia, Lamprakis, Christos, Theodoropoulou, Anastasia, Doerr, Stefan, Chatzigoulas, Alexios, Manchester, John, Velez-Vega, Camilo, Duca, José S, Cournia, Zoe
Published in The journal of physical chemistry. B (24.02.2022)
Published in The journal of physical chemistry. B (24.02.2022)
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Pyrazolo[1,5- a]pyrimidine-based inhibitors of HCV polymerase
Popovici-Muller, Janeta, Shipps, Gerald W., Rosner, Kristin E., Deng, Yongqi, Wang, Tong, Curran, Patrick J., Brown, Meredith A., Siddiqui, M. Arshad, Cooper, Alan B., Duca, José, Cable, Michael, Girijavallabhan, Viyyoor
Published in Bioorganic & medicinal chemistry letters (15.11.2009)
Published in Bioorganic & medicinal chemistry letters (15.11.2009)
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Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease
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
Published in Chemical Science (28.01.2021)
Published in Chemical Science (28.01.2021)
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Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations
Velez-Vega, Camilo, McKay, Daniel J. J, Kurtzman, Tom, Aravamuthan, Vibhas, Pearlstein, Robert A, Duca, José S
Published in Journal of chemical theory and computation (10.11.2015)
Published in Journal of chemical theory and computation (10.11.2015)
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