In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. - Edson Luiz Folador; Paulo Vinícius Sanches Daltro de Carvalho; Wanderson Marques Silva; Rafaela Salgado Ferreira; Artur Silva; M. Michael Gromiha; Preetam Ghosh; Debmalya Barh; Vasco Ariston de Carvalho Azevedo; Richard Röttger (BMC Syst. Biol., 2016)

Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations. - Raoni Almeida de Souza; Natalia Díaz; Ronaldo Alves Pinto Nagem; Rafaela Salgado Ferreira; Dimas Suárez (J. Comput. Aided Mol. Des., 2016)

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations. - Luan Carvalho Martins; Pedro Henrique Monteiro Torres; Renata Barbosa de Oliveira; Pedro Geraldo Pascutti; Elio A. Cino; Rafaela Salgado Ferreira (J. Comput. Aided Mol. Des., 2018)

Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. - Lucianna Helene Santos; Birgit J. Waldner; Julian E. Fuchs; Glaécia A. N. Pereira; Klaus R. Liedl; Ernesto Raúl Caffarena; Rafaela Salgado Ferreira (J. Chem. Inf. Model., 2019)

Discovery of Potent, Reversible, and Competitive Cruzain Inhibitors with Trypanocidal Activity: A Structure-Based Drug Design Approach. - Mariana Laureano de Souza; Celso de Oliveira Rezende Junior; Rafaela Salgado Ferreira; Rocio Marisol Espinoza Chávez; Leonardo L. G. Ferreira; Brian W. Slafer; Luma G. Magalhães; Renata Krogh; Glaucius Oliva; Fabio Cardoso Cruz; Luiz Carlos Dias; Adriano D. Andricopulo (J. Chem. Inf. Model., 2020)

nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale. - Alexandre V. Fassio; Lucianna Helene Santos; Sabrina de Azevedo Silveira; Rafaela Salgado Ferreira; Raquel Cardoso de Melo Minardi (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Prioritizing Virtual Screening with Interpretable Interaction Fingerprints. - Alexandre V. Fassio; Laura Shub; Luca Ponzoni; Jessica McKinley; Matthew J. O'Meara; Rafaela Salgado Ferreira; Michael J. Keiser; Raquel Cardoso de Melo Minardi (J. Chem. Inf. Model., 2022)

Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2. - Lucianna Helene Santos; Thales Kronenberger; Renata G. Almeida; Elany B. Silva; Rafael E. O. Rocha; Joyce C. Oliveira; Luiza V. Barreto; Danielle Skinner; Pavla Fajtová; Miriam A. Giardini; Brendon Woodworth; Conner Bardine; et al. (J. Chem. Inf. Model., 2022)

Characterization of an Allosteric Pocket in Zika Virus NS2B-NS3 Protease. - Naiá Porã Santos; Lucianna Helene Santos; Mariana Torquato Quezado de Magalhães; Jian Lei; Rolf Hilgenfeld; Rafaela Salgado Ferreira; Lucas Bleicher (J. Chem. Inf. Model., 2022)

Experimental and Computational Study of Aryl-thiosemicarbazones Inhibiting Cruzain Reveals Reversible Inhibition and a Stepwise Mechanism. - Luan Carvalho Martins; Renata Barbosa de Oliveira; Jerônimo Lameira; Rafaela Salgado Ferreira (J. Chem. Inf. Model., 2023)

Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. - Mateus Sá Magalhães Serafim; Thales Kronenberger; Rafael Eduardo Oliveira Rocha; Amanda Del Rio Abreu Rosa; Thaysa Lara Gonçalves Mello; Antti Poso; Rafaela Salgado Ferreira; Jonatas Santos Abrahão; Erna Geessien Kroon; Bruno Eduardo Fernandes Mota; Vinicius Gonçalves Maltarollo (J. Chem. Inf. Model., 2024)