3D Protein Structure Predicted from Sequence - Debora S. Marks; Lucy J. Colwell; Robert P. Sheridan; Thomas A. Hopf; Andrea Pagnani; Riccardo Zecchina; Chris Sander (CoRR, 2011)

Homology-based inference sets the bar high for protein function prediction. - Tobias Hamp; Rebecca Kassner; Stefan Seemayer; Esmeralda Vicedo; Christian Schaefer; Dominik Achten; Florian Auer; Ariane Boehm; Tatjana Braun; Maximilian Hecht; Mark Heron; Peter Hönigschmid; et al. (BMC Bioinform., 2013)

FreeContact: fast and free software for protein contact prediction from residue co-evolution. - László Kaján; Thomas A. Hopf; Matú Kala; Debora S. Marks; Burkhard Rost (BMC Bioinform., 2014)

Population-specific design of de-immunized protein biotherapeutics. - Benjamin Schubert; Charlotta Schärfe; Pierre Dönnes; Thomas A. Hopf; Debora S. Marks; Oliver Kohlbacher (PLoS Comput. Biol., 2018)

The EVcouplings Python framework for coevolutionary sequence analysis. - Thomas A. Hopf; Anna G. Green; Benjamin Schubert; Sophia Mersmann; Charlotta Schärfe; John Ingraham; Ágnes Tóth-Petróczy; Kelly Brock; Adam J. Riesselman; Perry Palmedo; Chan Kang; Robert P. Sheridan; et al. (Bioinform., 2019)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)