KVFinder: steered identification of protein cavities as a PyMOL plugin. - Saulo Henrique Pires de Oliveira; Felipe A. N. Ferraz; Rodrigo V. Honorato; José Xavier-Neto; Tiago José P. Sobreira; Paulo S. L. de Oliveira (BMC Bioinform., 2014)

CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database. - Rodrigo V. Honorato (J. Open Source Softw., 2016)

ParKVFinder: A thread-level parallel approach in biomolecular cavity detection. - João Victor da Silva Guerra; Helder Veras Ribeiro filho; Leandro Oliveira Bortot; Rodrigo Vargas Honorato; José Geraldo de Carvalho Pereira; Paulo Sérgio Lopes-de-Oliveira (SoftwareX, 2020)

Structural biology in the clouds: The WeNMR-EOSC Ecosystem. - Rodrigo Vargas Honorato; Panagiotis I. Koukos; Brian Jiménez-García; Andrei Tsaregorodtsev; Marco Verlato; Andrea Giachetti 002; Antonio Rosato; Alexandre M. J. J. Bonvin (CoRR, 2021)

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)