MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. - Richard J. Gowers; Max Linke; Jonathan Barnoud; Tyler J. E. Reddy; Manuel N. Melo; Sean L. Seyler; Jan J. Domanski; David L. Dotson; Sébastien Buchoux; Ian M. Kenney; Oliver Beckstein (SciPy, 2016)

Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies. - Filipe M. Sousa; Luís M. P. Lima; Clément Arnarez; Manuela M. Pereira; Manuel N. Melo (J. Chem. Inf. Model., 2021)

Lipid Shape as a Membrane Activity Modulator of a Fusogenic Antimicrobial Peptide. - Marcin Makowski; Octávio L. Franco; Nuno C. Santos; Manuel N. Melo (J. Chem. Inf. Model., 2025)