PEN-ASSEMBLE v0.5.1

Programmable Enzyme Networks - Automated Strategy and Scoring Engine for Molecular Bridge-recombinase Library Engineering

Part of PEN-STACK: genome-atlas -> mech-class -> pen-score -> pen-assemble -> PEN-COMPARE

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PEN-ASSEMBLE is the computational nomination pipeline for IS110-family bridge recombinase design. It generates and evaluates 1,029 candidate designs across four orthogonal engineering strategies - domain-swap chimeras, IS110 ortholog discovery, Monte Carlo deimmunization, and ProteinMPNN backbone redesign - using the 8-axis PenScore composite metric (pen-score v0.1.2). The pipeline is pre-registered, fully reproducible, and produces wet-lab synthesis sheets ready for experimental validation.

Note

All five pre-registered predictions PASS (5/5). 16 designs beat IS621 verbatim lockpoint (PenScore > 0.929). See Pre-Registered Predictions.

Contents

• Quick Start
  • Installation
  • Generating the catalog
  • Loading the catalog in Python
  • Computing PenScore
  • Codon optimisation
  • Running the pre-registered prediction tests
  • Running the test suite
• API Reference
  • pen_assemble.pen_score
  • pen_assemble.catalog
  • pen_assemble.codon
• Pre-Registered Predictions
  • P5 Top-5 Designs
  • Bootstrap Analysis
• Methodology Notes
  • Note 1 - Rosetta ΔΔG for D8PEA4 / D7BKC8 (cross-protein invalid)
  • Note 2 - Rosetta stability gate universally non-functional
  • Note 3 - MHCflurry version shift
  • Note 4 - P3 reference corrected
  • Note 5 - P5 diversity enforcement
  • Note 6 - Gate 8 ATLAS novelty not evaluated for Strategy B
• Changelog
  • v0.5.0 (2026-05-20)

Quick links

• Index

• Module Index

• API Reference

• GitHub

• genome-atlas

• mech-class

• pen-score