Generation of a consensus protein domain dictionary. - R. Dustin Schaeffer; Amanda L. Jonsson; Andrew M. Simms; Valerie Daggett (Bioinform., 2011)

ECOD: An Evolutionary Classification of Protein Domains. - Hua Cheng; R. Dustin Schaeffer; Yuxing Liao; Lisa N. Kinch; Jimin Pei; Shuoyong Shi; Bong-Hyun Kim; Nick V. Grishin (PLoS Comput. Biol., 2014)

ECOD: new developments in the evolutionary classification of domains. - R. Dustin Schaeffer; Yuxing Liao; Hua Cheng; Nick V. Grishin (Nucleic Acids Res., 2017)

A sequence family database built on ECOD structural domains. - Yuxing Liao; R. Dustin Schaeffer; Jimin Pei; Nick V. Grishin (Bioinform., 2018)

Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. - Kirill E. Medvedev; Lisa N. Kinch; R. Dustin Schaeffer; Nick V. Grishin (PLoS Comput. Biol., 2019)

ECOD Classification of AFDB 48 Proteomes. - R. Dustin Schaeffer; Jing Zhang 115; Kirill E. Medvedev; Qian Cong; Nick V. Grishin (Zenodo, 2023)

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. - R. Dustin Schaeffer; Jing Zhang; Kirill E. Medvedev; Lisa N. Kinch; Qian Cong; Nick V. Grishin (PLoS Comput. Biol., 2024)

Leveraging AI to explore structural contexts of post-translational modifications in drug binding. - Kirill E. Medvedev; R. Dustin Schaeffer; Nick V. Grishin (J. Cheminformatics, 2025)