Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization. - Carl D. Elkin; Harmon J. Zuccola; James M. Hogle; Diane Joseph-McCarthy (J. Comput. Aided Mol. Des., 2000)

Functional group placement in protein binding sites: a comparison of GRID and MCSS. - Ryan Bitetti-Putzer; Diane Joseph-McCarthy; James M. Hogle; Martin Karplus (J. Comput. Aided Mol. Des., 2001)

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4. - Erik Evensen; Diane Joseph-McCarthy; Gregory A. Weiss; Stuart L. Schreiber; Martin Karplus (J. Comput. Aided Mol. Des., 2007)

CONFIRM: connecting fragments found in receptor molecules. - David C. Thompson 002; Rajiah Aldrin Denny; Ramaswamy Nilakantan; Christine Humblet; Diane Joseph-McCarthy; Eric Feyfant (J. Comput. Aided Mol. Des., 2008)

Investigation of MM-PBSA Rescoring of Docking Poses. - David C. Thompson 002; Christine Humblet; Diane Joseph-McCarthy (J. Chem. Inf. Model., 2008)

Challenges of fragment screening. - Diane Joseph-McCarthy (J. Comput. Aided Mol. Des., 2009)

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide. - Sameer Kawatkar; Hongming Wang; Ryszard Czerminski; Diane Joseph-McCarthy (J. Comput. Aided Mol. Des., 2009)

Virtual fragment screening: exploration of MM-PBSA re-scoring. - Sameer Kawatkar; Demetri Moustakas; Matthew Miller; Diane Joseph-McCarthy (J. Comput. Aided Mol. Des., 2012)

Ensemble-Based Docking Using Biased Molecular Dynamics. - Arthur J. Campbell; Michelle L. Lamb; Diane Joseph-McCarthy (J. Chem. Inf. Model., 2014)

Fragment-Based Lead Discovery and Design. - Diane Joseph-McCarthy; Arthur J. Campbell; Gunther Kern; Demetri Moustakas (J. Chem. Inf. Model., 2014)

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. - Alexander S. Bayden; Demetri T. Moustakas; Diane Joseph-McCarthy; Michelle L. Lamb (J. Chem. Inf. Model., 2015)

Computational identification of antibody-binding epitopes from mimotope datasets. - Rang Li; Sabrina Wilderotter; Madison Stoddard; Debra Van Egeren; Arijit Chakravarty; Diane Joseph-McCarthy (Frontiers Bioinform., 2024)

Automating biomedical literature review for rapid drug discovery: Leveraging GPT-4 to expedite pandemic response. - Jingmei Yang; Kenji C. Walker; Ayse A. Bekar-Cesaretli; Boran Hao; Nahid Bhadelia; Diane Joseph-McCarthy; Ioannis Ch. Paschalidis (Int. J. Medical Informatics, 2024)

Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. - Ayse A. Bekar-Cesaretli; Omeir Khan; Thu Nguyen; Dima Kozakov; Diane Joseph-McCarthy; Sandor Vajda (J. Chem. Inf. Model., 2024)

Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. - Omeir Khan; George Jones; Maria Lazou; Diane Joseph-McCarthy; Dima Kozakov; Dmitri Beglov; Sandor Vajda (J. Chem. Inf. Model., 2024)

Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface. - Maria Lazou; Jonathan R. Hutton; Arijit Chakravarty; Diane Joseph-McCarthy (J. Comput. Aided Mol. Des., 2024)