Institute for Protein Design
Part of University of Washington
A University of Washington institute creating proteins from scratch, with computational design methods for therapeutics, vaccines, and nanomaterials.
Models (7)
Beta-Barrel Nanopore Design Model
Institute for Protein Design / University of Washington
Released June 4, 2026
Diffusion-based backbone generation and sequence design method for programmable asymmetric transmembrane beta-barrel nanopores.
All-atom protein design diffusion model conditioned on ligands, nucleic acids, and other non-protein atoms, supporting enzyme and DNA binder design.
Atom-level diffusion model for de novo enzyme design that scaffolds arbitrary active-site geometries without specifying catalytic residue positions.
Protein sequence design model that represents small molecules, nucleotides, and metals at atomic resolution, enabling ligand-aware enzyme design.
De novo protein design diffusion model that generates backbone structures conditioned on binding targets, symmetry constraints, and functional motifs.
AlphaFold fine-tuned on peptide-MHC and protein-peptide binding data for specificity prediction across MHC class I/II, PDZ, and SH3 domains.
Message passing neural network for fixed-backbone protein sequence design. Achieves 52.4% native sequence recovery, far surpassing Rosetta's 32.9%.