Construction of a Virtual High Throughput Screen by 4D-QSAR Analysis: Application to a Combinatorial Library of Glucose Inhibitors of Glycogen Phosphorylase b. - Anton J. Hopfinger; Andrea Reaka; Prabha Venkatarangan; José S. Duca; Shen Wang (J. Chem. Inf. Comput. Sci., 1999)

Estimation of Molecular Similarity Based on 4D-QSAR Analysis: Formalism and Validation. - José S. Duca; Anton J. Hopfinger (J. Chem. Inf. Comput. Sci., 2001)

4D-Fingerprints, Universal QSAR and QSPR Descriptors. - Craig L. Senese; José S. Duca; Dahua Pan; Anton J. Hopfinger; Yufeng J. Tseng (J. Chem. Inf. Model., 2004)

Cross-Docking of Inhibitors into CDK2 Structures. 1. - José S. Duca; Vincent S. Madison; Johannes H. Voigt (J. Chem. Inf. Model., 2008)

Cross-Docking of Inhibitors into CDK2 Structures. 2. - Johannes H. Voigt; Carl Elkin; Vincent S. Madison; José S. Duca (J. Chem. Inf. Model., 2008)

soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts. - Charles A. Lesburg; José S. Duca (Nucleic Acids Res., 2008)

Gazing into the crystal ball; the future of computer-aided drug design. - Eric J. Martin; Peter Ertl; Peter Hunt; José S. Duca; Richard Lewis (J. Comput. Aided Mol. Des., 2012)

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., 2014)

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; José S. Duca; Richard A. Lewis; Deborah A. Loughney; Eric S. Manas; Georgia B. McGaughey; Catherine E. Peishoff; Herman van Vlijmen (J. Comput. Aided Mol. Des., 2016)

Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules. - Callum J. Dickson; Viktor Hornak; Dallas Bednarczyk; José S. Duca (J. Chem. Inf. Model., 2019)

PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks. - José Jiménez; Davide Sabbadin; Alberto Cuzzolin; Gerard Martínez-Rosell; Jacob Gora; John Manchester; José S. Duca; Gianni De Fabritiis (J. Chem. Inf. Model., 2019)

Revealing Molecular Determinants of hERG Blocker and Activator Binding. - Callum J. Dickson; Camilo Velez-Vega; José S. Duca (J. Chem. Inf. Model., 2020)

Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots. - Callum J. Dickson; Viktor Hornak; José S. Duca (J. Chem. Inf. Model., 2021)

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; Hagen Münkler; Viktor Hornak; José S. Duca (J. Comput. Aided Mol. Des., 2024)