Structural descriptor database: a new tool for sequence-based functional site prediction. - Juliana S. Bernardes; Jorge H. Fernandez; Ana Tereza Ribeiro de Vasconcelos (BMC Bioinform., 2008)

AutoModel: A Client-Server Tool for Intuitive and Interactive Homology Modeling of Protein-Ligand Complexes. - João Luiz de Almeida Filho; Annabell Del Real Tamariz; Jorge H. Fernandez (BSB, 2018)

MDR SurFlexDock: A Semi-automatic Webserver for Discrete Receptor-Ensemble Docking. - João Luiz de Almeida Filho; Jorge Hernandez Fernandez (BSB, 2019)

In silico study of the impact of the PRKAG2-H401Q mutation on AMPK affinity for AMP and ATP. - Karine Terra de Souza; Glauber Monteiro Dias; Jorge Hernandez Fernandez (BSB, 2024)