Publications by authors named "Jose Duca"

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The current understanding of KRAS oligomerization on membranes.
Nastazia Lesgidou, Michail Papadourakis, Nishita Mandal, Sepehr Dehghani-Ghahnaviyeh, Camilo Velez-Vega, José S Duca

Curr Opin Struct Biol· December 2025

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Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design.
Aaron D Danilack, Callum J Dickson, Cihan Soylu, Mike Fortunato, Stephane Rodde, Jose S Duca

J Comput Aided Mol Des· May 2024

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Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications.
Panagiotis I Koukos, Sepehr Dehghani-Ghahnaviyeh, Camilo Velez-Vega, John Manchester, D Peter Tieleman, José S Duca

J Chem Theory Comput· December 2023

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Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability.
Ioannis Andreadelis, Sofia Kiriakidi, Christos Lamprakis, Anastasia Theodoropoulou, Stefan Doerr, José S Duca

J Phys Chem B· February 2022

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Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots.
Callum J Dickson, Viktor Hornak, Jose S Duca

J Chem Inf Model· December 2021

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Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments.
Christos Lamprakis, Ioannis Andreadelis, John Manchester, Camilo Velez-Vega, José S Duca

J Chem Theory Comput· May 2021

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Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.
Anna Pavlova, Diane L Lynch, Isabella Daidone, Laura Zanetti-Polzi, Micholas Dean Smith, José S Duca

Chem Sci· January 2021

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Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.
Anna Pavlova, Diane L Lynch, Isabella Daidone, Laura Zanetti-Polzi, Micholas Dean Smith, José S Duca

bioRxiv· September 2020

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Rethinking drug design in the artificial intelligence era.
Petra Schneider, W Patrick Walters, Alleyn T Plowright, Norman Sieroka, Jennifer Listgarten, José S Duca

Nat Rev Drug Discov· May 2020

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Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening.
Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J Dickson, Jose S Duca

PLoS One· February 2020

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Revealing Molecular Determinants of hERG Blocker and Activator Binding.
Callum J Dickson, Camilo Velez-Vega, Jose S Duca

J Chem Inf Model· January 2020

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A small-molecule inhibitor of C5 complement protein.
Keith Jendza, Mitsunori Kato, Michael Salcius, Honnappa Srinivas, Andrea De Erkenez, Jose Duca

Nat Chem Biol· July 2019

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PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks.
José Jiménez, Davide Sabbadin, Alberto Cuzzolin, Gerard Martínez-Rosell, Jacob Gora, José Duca

J Chem Inf Model· March 2019

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Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules.
Callum J Dickson, Viktor Hornak, Dallas Bednarczyk, Jose S Duca

J Chem Inf Model· January 2019

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Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology.
Robert A Pearlstein, Daniel J J McKay, Viktor Hornak, Callum Dickson, Andrei Golosov, José Duca

Curr Top Med Chem· September 2017

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"Addition" and "Subtraction": Selectivity Design for Type II Maternal Embryonic Leucine Zipper Kinase Inhibitors.
Xin Chen, John Giraldes, Elizabeth R Sprague, Subarna Shakya, Zhuoliang Chen, Jose Duca

J Med Chem· March 2017

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Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation.
Robert A Pearlstein, K Andrew MacCannell, Gül Erdemli, Sarita Yeola, Gabriel Helmlinger, José S Duca

Curr Top Med Chem· February 2017

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Structure-Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling.
Callum J Dickson, Viktor Hornak, Robert A Pearlstein, Jose S Duca

J Am Chem Soc· January 2017

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Collaborating to improve the use of free-energy and other quantitative methods in drug discovery.
Bradley Sherborne, Veerabahu Shanmugasundaram, Alan C Cheng, Clara D Christ, Renee L DesJarlais, Jose S Duca

J Comput Aided Mol Des· December 2016

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Uncoupling the Structure-Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding.
Callum J Dickson, Viktor Hornak, Camilo Velez-Vega, Daniel J J McKay, John Reilly, Jose S Duca

J Med Chem· June 2016

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Toward the Validation of Maternal Embryonic Leucine Zipper Kinase: Discovery, Optimization of Highly Potent and Selective Inhibitors, and Preliminary Biology Insight.
B Barry Touré, John Giraldes, Troy Smith, Elizabeth R Sprague, Yaping Wang, Jose Duca

J Med Chem· May 2016

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Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.
Camilo Velez-Vega, Daniel J J McKay, Tom Kurtzman, Vibhas Aravamuthan, Robert A Pearlstein, José S Duca

J Chem Theory Comput· November 2015

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Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2.
Syed Sohail Ahmed, Wayne Volkmuth, José Duca, Lorenzo Corti, Michele Pallaoro

Sci Transl Med· July 2015

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Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH.
Camilo Velez-Vega, Daniel J J McKay, Vibhas Aravamuthan, Robert Pearlstein, José S Duca

J Chem Inf Model· December 2014

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Modulating the interaction between CDK2 and cyclin A with a quinoline-based inhibitor.
Yongqi Deng, Gerald W Shipps, Lianyun Zhao, M Arshad Siddiqui, Janeta Popovici-Muller, Jose S Duca

Bioorg Med Chem Lett· January 2014

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