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All papers authored by Jose Duca

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2022 Alexios Chatzigoulas, Ioannis Andreadelis, Stefan Doerr, Christos Lamprakis, Anastasia Theodoropoulou, John Manchester, Camilo Velez-Vega, Jose Duca

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, Zoe Cournia

Evaluation of K-Ras4B dimer interfaces and the role of Raf effectors

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2021 Hongbin Wan, Vibhas Aravamuthan, Sarah Williams, Charles Wartchow, José S. Duca

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, Robert A. Pearlstein

Solvation dynamics-powered structure and function of multi-molecular cellular systems exemplified by non-equilibrium cereblon-degrader-CK1α ternary complex formation

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Christos Lamprakis, Ioannis Andreadelis, John Manchester, Camilo Velez-Vega, José S. Duca

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Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

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Anna Pavlova

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, Diane L. Lynch, Isabella Daidone

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, Laura Zanetti-Polzi

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, Micholas Dean Smith, Chris Chipot, Daniel W. Kneller

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, Andrey Kovalevsky

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, Leighton Coates

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, Andrei A. Golosov, Callum J. Dickson, Jeremy C. Smith, Camilo Velez-Vega, Jose S. Duca

ORCID

, Josh V. Vermaas

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and 5 other authors

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

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2019 Callum J. Dickson

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, Camilo Velez-Vega, Jose S. Duca

ORCID

Revealing Molecular Determinants of hERG Blocker and Activator Binding

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Petra Schneider, W. Patrick Walters, Alleyn T. Plowright, Norman Sieroka, Jennifer Listgarten

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, Robert A. Goodnow, Jasmin Fisher

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, Johanna M. Jansen, José S. Duca

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, Thomas S. Rush, Matthias Zentgraf, John Edward Hill, Elizabeth Krutoholow, Matthias Kohler, Jeff Blaney and 3 other authors

Rethinking drug design in the artificial intelligence era

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Keith Jendza, Mitsunori Kato

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, Michael Salcius, Honnappa Srinivas, Andrea De Erkenez, Anh Nguyen, Doug McLaughlin, Celine Be, Christian Wiesmann, Jason Murphy, Philippe Bolduc

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, Muneto Mogi, Jose Duca

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, Abdel Namil, Michael Capparelli and 12 other authors

A small-molecule inhibitor of C5 complement protein

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Lieyang Chen

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ORCID

, Steven Ramsey, Callum J. Dickson, José S S. Duca

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, Viktor Hornak, David R. Koes, Tom Kurtzman

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Hidden Bias in the DUD-E Dataset Leads to Misleading Performance of Deep Learning in Structure-Based Virtual Screening

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2018 José Jiménez

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, Davide Sabbadin, Alberto Cuzzolin, Gerard Martínez-Rosell, Jacob Gora, John Manchester, José Duca

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, Gianni De Fabritiis

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PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks

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Callum J. Dickson

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, Viktor Hornak, Dallas Bednarczyk, Jose S. Duca

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Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules

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2017 Robert A. Pearlstein, Daniel J. J. McKay, Viktor Hornak, Callum Dickson, Andrei Golosov, Tyler Harrison, Camilo Velez-Vega, José Duca

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Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology

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Xin Chen

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, John Giraldes, Elizabeth R. Sprague, Subarna Shakya, Zhuoliang Chen, Yaping Wang, Carol Joud, Simon Mathieu, Christine Hiu-Tung Chen, Christopher Straub, Jose Duca

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, Kristen Hurov, Yanqiu Yuan, Wenlin Shao, B. Barry Touré

“Addition” and “Subtraction”: Selectivity Design for Type II Maternal Embryonic Leucine Zipper Kinase Inhibitors

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2016 Callum J. Dickson

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, Viktor Hornak, Robert A. Pearlstein, Jose S. Duca

ORCID

Structure-kinetic relationships of passive membrane permeation from multiscale modeling

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Bradley Sherborne, Veerabahu Shanmugasundaram

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, Alan C. Cheng, Clara D. Christ, Renee L. DesJarlais, Jose S. Duca

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, Richard A. Lewis, Deborah A. Loughney, Eric S. Manas, Georgia B. McGaughey, Catherine E. Peishoff, Herman van Vlijmen

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

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Callum J. Dickson, Viktor Hornak, Camilo Velez-Vega, Daniel J. J. McKay, John Reilly, David A. Sandham, Duncan Shaw, Robin A. Fairhurst, Steven J. Charlton, David A. Sykes, Robert A. Pearlstein, Jose S. Duca

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Uncoupling the Structure–Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding

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B. Barry Touré, John Giraldes, Troy Smith, Elizabeth R. Sprague, Yaping Wang, Simon Mathieu, Zhuoliang Chen, Yuji Mishina, Yun Feng, Yan Yan-Neale, Subarna Shakya, Dongshu Chen, Matthew Meyer, David Puleo, J. Tres Brazell and 11 other authors

Toward the Validation of Maternal Embryonic Leucine Zipper Kinase: Discovery, Optimization of Highly Potent and Selective Inhibitors, and Preliminary Biology Insight

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Robert A. Pearlstein, Robert Pearlstein, K. Andrew MacCannell, Gül Erdemli, Sarita Yeola, Gabriel Helmlinger, Qi-Ying Hu, Ramy Farid, William Egan, Steven Whitebread, Clayton Springer, Jeremy Beck, Hao-Ran Wang, Mateusz Maciejewski, Laszlo Urban and 2 other authors

Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation

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2015 Camilo Velez-Vega, Daniel J. J. McKay, Tom Kurtzman, Vibhas Aravamuthan, Robert A. Pearlstein, José S. Duca

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Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations

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A. Becker-Heck, A. Bizet, R. Ryan, P. Krug, E. Filhol, B. Linghu, E. Oakeley, F. Serluca, F. Legendre, N. Dörner, Mc Lasbennes, J. Duca

ORCID

, F. Yang, A. Damask, L. Klickstein and 19 other authors

Identification of human mutations in TRAF3IP1 in patients with nephronophthisis and retinal degeneration

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Syed Sohail Ahmed, Ahmed Ss, Wayne Volkmuth, Jose Duca

ORCID

, Lorenzo Corti, Michele Pallaoro, Alfredo Pezzicoli, Anette Karle, Fabio Rigat, Rino Rappuoli, Vas Narasimhan, Ilkka Julkunen, Arja Vuorela, Outi Vaarala, Hanna Nohynek and 8 other authors

Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2

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