Software
Over the years I have contributed to the development of several tools and webservices:
RMSX and Flipbook
A user-friendly and intuitive high-resolution mapping of molecular motions over time, combining features from both RMSD and RMSF, and supporting visualizations through both VMD and UCSF ChimeraX. This is work lead by Finn Beruldsen in collaboration with Martiela Vaz de Freitas.
CrossDome
An interactive R package to predict T-cell off-target toxicity risk for therapeutic peptides or TCRs, using immunopeptidomics databases. This tool was implemented by Andre Fonseca.
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.
EnGens
A computational framework for generation and analysis of representative protein conformational ensembles. Work in collaboration with 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.