Software
Over the years I have contributed to the development of several tools and webservices:
HLA-Arena
A customizable environment for the structural modeling and analysis of peptide-HLA complexes. This is joint work with Jayvee Abella, Sarah Hall-Swan Anja Conev and many others.
DINC-COVID
A web server for ensemble docking of potential inhibitors to SARS-CoV-2 proteins. This is joint work with Sarah Hall-Swan, Geancarlo Zanatta, Maurício Rigo and others.
DINC
A web server for incremental molecular docking of large ligands and peptides. This is joint work with Didier Devaurs, Mark Moll, Sarah Hall-Swan, Ankur Dhanik and several others.
APE-Gen
A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations. This is joint work with Jayvee Abella.
pHLA-RF
A Random Forest Classifier to predict HLA binders using APE-Gen models. This is joint work with Jayvee Abella.
DockTope
An automated docking-based method for structural prediction of pMHC complexes. This is joint work with Maurício Rigo, Gustavo Vieira, Marialva Sinigalia, Jason Greenbaum, Jason Yan and several others.
CrossTope
A curate repository of pMHC structures, focused on immunogenicity and cross-reactivity. This is joint work with Maurício Rigo, Gustavo Vieira, Marialva Sinigalia and several others.