João Rodrigues

This study uses cryo-EM to reveal structural plasticity and ligand promiscuity of CYP3A4, showing multiple conformations and highlighting the F/G loop's role in binding pocket remodeling.

The paper evaluates sequence- and structure-based methods to predict specificity-determining positions in Axl complexes, finding sequence-based methods overpredict and that combining them with HADDOCK improves predictions.

This study uses structural modeling to analyze ACE2 orthologs and their interactions with SARS-CoV-2 spike protein, identifying mutations that affect susceptibility and suggesting therapeutic applications.

The paper introduces a coarse-grained modeling approach in HADDOCK to predict large biomolecular assemblies, achieving faster calculations with maintained accuracy.

pdb-tools provides command-line Python scripts for editing, converting, and validating PDB files without external dependencies.