Dario F. Marzella

The paper introduces a fast computational docking protocol for TCRpMHC-I complexes, achieving faster modeling and better model quality than existing tools.

IMMREP25 evaluates TCR:pMHC binding prediction for unseen peptides, showing improved performance with structural modeling but still below random guessing.

The paper updates PANDORA to predict bidirectional peptide conformations for MHC class II, achieving low RMSD values for reversed-bound peptides.

PANDORA v2.0 benchmarks peptide-MHC II modeling software and improves its performance and usability for generating 3D pMHC-II structures.

This paper improves MHC-I binding peptide prediction generalizability using geometric deep learning, outperforming sequence-based methods without binding affinity data.

PANDORA is a fast pMHC structure modelling pipeline that uses anchor restraints to generate accurate models with high success rate and speed.

DeepRank uses 3D CNNs to mine protein-protein interfaces, achieving competitive or better performance in classification and docking model ranking.