Kinact: a computational approach for predicting activating missense mutations in protein kinases. - Carlos H. M. Rodrigues; David B. Ascher; Douglas E. V. Pires (Nucleic Acids Res., 2018)

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2018)

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. - Carlos H. M. Rodrigues; Yoochan Myung; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2019)

mCSM-AB2: guiding rational antibody design using graph-based signatures. - Yoochan Myung; Carlos H. M. Rodrigues; David B. Ascher; Douglas E. V. Pires (Bioinform., 2020)

EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. - Douglas E. V. Pires; Wandré N. P. Veloso; Yoochan Myung; Carlos H. M. Rodrigues; Michael Silk; Pâmela M. Rezende; Francislon Silva; Joicymara S. Xavier; João P. L. Velloso; Carlos Henrique da Silveira; David B. Ascher (Bioinform., 2020)

mCSM-membrane: predicting the effects of mutations on transmembrane proteins. - Douglas E. V. Pires; Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2020)

Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis. - Edward Airey; Stephanie Portelli; Joicymara S. Xavier; Yoochan Myung; Michael Silk; Malancha Karmakar; João P. L. Velloso; Carlos H. M. Rodrigues; Hardik H. Parate; Anjali Garg; Raghad Al-Jarf; Lucy Barr; et al. (Artificial Neural Networks, 3rd Edition, 2021)

pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2021)

mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2021)

MTR3D: identifying regions within protein tertiary structures under purifying selection. - Michael Silk; Douglas E. V. Pires; Carlos H. M. Rodrigues; Elston N. D'souza; Moshe Olshansky; Natalie Thorne; David B. Ascher (Nucleic Acids Res., 2021)

Structural landscapes of PPI interfaces. - Carlos H. M. Rodrigues; Douglas E. V. Pires; Tom L. Blundell; David B. Ascher (Briefings Bioinform., 2022)

CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. - Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2022)

DockNet: high-throughput protein-protein interface contact prediction. - Nathan P. Williams; Carlos H. M. Rodrigues; Jia Truong; David B. Ascher; Jessica K. Holien (Bioinform., 2023)

DDMut: predicting effects of mutations on protein stability using deep learning. - Yunzhuo Zhou; Qisheng Pan; Douglas E. V. Pires; Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2023)

piscesCSM: prediction of anticancer synergistic drug combinations. - Raghad Al-Jarf; Carlos H. M. Rodrigues; Yoochan Myung; Douglas E. V. Pires; David B. Ascher (J. Cheminformatics, 2024)