AVID: An integrative framework for discovering functional relationships among proteins. - Taijiao Jiang; Amy E. Keating (BMC Bioinform., 2005)

Paircoil2: improved prediction of coiled coils from sequence. - A. V. McDonnell; Taijiao Jiang; Amy E. Keating; Bonnie Berger (Bioinform., 2006)

Ultra-Fast Evaluation of Protein Energies Directly from Sequence. - Gevorg Grigoryan; Fei Zhou 002; Steve R. Lustig; Gerbrand Ceder; Dane Morgan; Amy E. Keating (PLoS Comput. Biol., 2006)

Cluster expansion models for flexible-backbone protein energetics. - James R. Apgar; Seungsoo Hahn; Gevorg Grigoryan; Amy E. Keating (J. Comput. Chem., 2009)

Identifying and reducing error in cluster-expansion approximations of protein energies. - Seungsoo Hahn; Orr Ashenberg; Gevorg Grigoryan; Amy E. Keating (J. Comput. Chem., 2010)

Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins. - Joe DeBartolo; Mikko Taipale; Amy E. Keating (PLoS Comput. Biol., 2014)

Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions. - Vladimir Potapov; Jenifer B. Kaplan; Amy E. Keating (PLoS Comput. Biol., 2015)

TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs. - Alex J. Li; Vikram Sundar; Gevorg Grigoryan; Amy E. Keating (CoRR, 2022)