Skip to content

Research & Projects

Advancing the frontiers of bioinformatics

We work at the interface of computation and the life sciences, creating methods, algorithms, and software to understand how biomolecules interact and function.

Every research line walks hand in hand with engineering: many of our projects produce open tools and databases used by the scientific community worldwide.

Ongoing

Current projects

Active research lines and the software born from them. The lab follows a research → tool → publication cycle.

Ongoing

Peptide–protein interface atlas

Large-scale structural characterization of peptide–protein complexes, with graph-based signatures to support peptide design.

PeptidesInterfacesGraphs
Tools: Propedia2 · Propedia
Output: Propedia v2.3 (2023)
Ongoing

RNA–protein interaction structures

Organizing and analyzing RNA–protein interaction structures in a public database, opening the way to new discoveries.

RNAStructuresDatabase
Tools: RNApedia
Output: RNApedia (2024)
Ongoing

Analogous & optimized molecular contacts

Detecting, comparing, and optimizing contacts in protein structures and complexes, accelerating structural analysis.

ContactsStructuresAlgorithms
Tools: VTR · COCaDA · nAPOLI
Output: COCaDA (2024) · VTR (2021)
Ongoing

Enzyme engineering & mutation effects

Modeling the impact of mutations on proteins and enzymes, with emphasis on beta-glucosidases and biotechnologically relevant variants.

EnzymesMutationsModeling
Tools: Glutantbase · E-Volve · SSV · MutaGraph
Output: Glutantbase (2020) · E-Volve (2022)
Ongoing

AI for drug discovery & peptides

Machine-learning models to prioritize candidates, predict interactions, and accelerate the discovery cycle. [Summary to be reviewed by the lab]

Machine LearningDrug discoveryPeptides
Output: Expanding research line
Ongoing

Scientific visualization & software

Platforms to manipulate, normalize, and visualize structures and mutations, making complex data accessible and reproducible.

VisualizationSoftwareReproducibility
Tools: PDBest · VERMONT · Proteus
Output: PDBest · VERMONT · Proteus