pdb-tools: a swiss army knife for molecular structures. - João P. G. L. M. Rodrigues; João M. C. Teixeira; Mikaël Trellet; Alexandre M. J. J. Bonvin (F1000Research, 2018)

Insights on cross-species transmission of SARS-CoV-2 from structural modeling. - João P. G. L. M. Rodrigues; Susana Barrera-Vilarmau; João M. C. Teixeira; Marija Sorokina; Elizabeth Seckel; Panagiotis L. Kastritis; Michael Levitt 001 (PLoS Comput. Biol., 2020)

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Zi Hao Liu; Oufan Zhang; João M. C. Teixeira; Jie Li 072; Teresa Head-Gordon; Julie D. Forman-Kay (Zenodo, 2023)

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Zi Hao Liu; Oufan Zhang; João M. C. Teixeira; Jie Li 072; Teresa Head-Gordon; Julie D. Forman-Kay (J. Open Source Softw., 2023)

FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins. - András Hatos; João M. C. Teixeira; Susana Barrera-Vilarmau; Attila Horvath; Silvio C. E. Tosatto; Michele Vendruscolo; Mónika Fuxreiter (Nucleic Acids Res., 2023)

Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments. - Zi Hao Liu; João M. C. Teixeira; Oufan Zhang; Thomas E. Tsangaris; Jie Li 072; Claudiu C. Gradinaru; Teresa Head-Gordon; Julie D. Forman-Kay (Bioinform., 2023)

DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning. - Giulia Crocioni; Dani L. Bodor; Coos Baakman; Farzaneh M. Parizi; Daniel-T. Rademaker; Gayatri Ramakrishnan; Sven van der Burg; Dario F. Marzella; João M. C. Teixeira; Li C. Xue (J. Open Source Softw., 2024)

HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes. - Marco Giulini; Victor Reys; João M. C. Teixeira; Brian Jiménez-García; Rodrigo V. Honorato; Anna Kravchenko; Xiaotong Xu; Raphaëlle Versini; Anna Engel; Stefan Verhoeven; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2025)