PeptideArena v1.0.0: De-Novo Peptide Inverse Folding
Abstract
Initial public release of PeptideArena, a benchmark of de novo peptide-binder backbone templates for inverse-folding evaluation. Contents 353 two-chain peptide–receptor PDB complexes 12 protein targets Peptide backbone lengths of 8, 16, and 24 residues Chain A: backbone-only poly-glycine designed peptide Chain B: fixed receptor context Intended use Design a sequence for chain A conditioned on chain B, refold the resulting peptide–receptor complex with a structure predictor of choice (e.g., Boltz-2 or OpenDDE), and evaluate target-aligned peptide backbone self-consistency RMSD. PeptideArena is not a sequence-recovery benchmark: chain A has no native sequence. Citation If you use PeptideArena, please cite the accompanying AtomWeaver preprint: Kitaygorodsky A, Hostallero DE, Broom A, Layne E, Hwang S, Kanawaty AK, Babej T, Butterfoss GL, Fingerhuth M. AtomWeaver: Multi-Component Flow Matching with a Structured Geometric Prior Facilitates Non-Canonical Peptide Design. bioRxiv. 2026. and this versioned release: Hostallero DE, Butterfoss G, Broom A, Hwang S, Layne E, Kanawaty A, Kitaygorodsky A, Fingerhuth M. PeptideArena v1.0.0: De-Novo Peptide Inverse Folding [computer software]. Version v1.0.0. Zenodo; 2026. doi:10.5281/zenodo.22922294.
