Changelog

v0.5.0 (2026-05-20)

First public release.

Pipeline

  • Design sourcing: (1,041 designs across 4 strategies), PenScore computation, ESMFold structural predictions, MHCflurry 2.2.1 immunogenicity scoring.

  • Eight-gate triage: (1,029 survivors), bootstrap rank stability, diversity analysis, failure-mode analysis.

  • Five pre-registered formal prediction tests (all PASS).

  • Public catalog: - CSV/Parquet scorecard, FASTA files, 1,029 per-design JSONs, self-contained HTML browser, wet-lab Markdown references.

Package

  • pen_assemble.pen_score - PenScore formula, IS621 lockpoints.

  • pen_assemble.catalog - catalog loading utilities.

  • pen_assemble.codon - codon optimisation, restriction-site scanner.

  • Test suite: 55+ unit tests (pytest).

  • Sphinx documentation.

Key results

  • 16 designs beat IS621 verbatim lockpoint (0.929).

  • IS621_deimmunized_v2 achieves PenScore = 0.9673.

  • 992 Strategy B IS110 orthologs pass all triage gates.

  • 5/5 pre-registered predictions PASS.

Disclosed deviations

  • Rosetta stability gate non-functional (universal, all 47 designs) - auto-passed.

  • P3 IS621 reference corrected from 0.250 to 0.7594.

  • P5 rank-5 diversity-enforced (A_007 replaces D023).

  • Gate 8 ATLAS not evaluated for Strategy B.