Protein Engineering Workflows

CWL workflows combining protein structure prediction and stability analysis for protein engineering applications.

Overview

This repository provides automated pipelines that combine:

Sequence → Structure Prediction → Stability Analysis → Engineering Candidates
           (Boltz-2 or Chai-1)     (stabiliNNator)

Tool Capabilities

Tool	Input	Output	Purpose
Boltz-2	YAML/FASTA	PDB/mmCIF	Structure prediction with constraints
Chai-1	FASTA	PDB/mmCIF	Structure prediction
stabiliNNator	PDB/mmCIF	Annotated PDB	Stability analysis (proline/disulfide)

Available Workflows

Workflow	Structure Tool	Stability Tools	Use Case
protein_stability_pipeline.cwl	boltz	stabilinnator (dynamic)	Simple usage, single analysis
protein_stability_with_chai.cwl	chai-lab	stabilinnator (dynamic)	Chai-1 alternative
protein_stability_explicit.cwl	boltz	prolinnator + disulfinnate	Explicit parallel analysis
protein_stability_explicit_chai.cwl	chai-lab	prolinnator + disulfinnate	Chai-1 explicit parallel
protein_stability_app.cwl	App-Boltz.pl	App-StabiliNNator.pl × 2	BV-BRC integration
protein_stability_app_chai.cwl	App-ChaiLab.pl	App-StabiliNNator.pl × 2	BV-BRC Chai-1 integration

Quick Start

# Install cwltool
pip install cwltool

# Run the stability pipeline with Boltz
cwltool cwl/workflows/protein_stability_pipeline.cwl examples/crambin_job.yml

# Run the alternative pipeline with Chai-1
cwltool cwl/workflows/protein_stability_with_chai.cwl examples/crambin_fasta_job.yml

# Run explicit workflow (parallel proline + disulfide analysis)
cwltool cwl/workflows/protein_stability_explicit.cwl examples/crambin_job.yml

# Run Chai-1 explicit workflow
cwltool cwl/workflows/protein_stability_explicit_chai.cwl examples/crambin_fasta_job.yml

# Run BV-BRC App script workflow
cwltool cwl/workflows/protein_stability_app.cwl examples/crambin_job.yml

Scientific Use Cases

Therapeutic Protein Stabilization

Improve shelf-life and thermal stability of biologic drugs by identifying:

• Residues to mutate to proline (reduce flexibility)
• Cysteine pairs for engineered disulfide bonds

Vaccine Antigen Design

Stabilize viral proteins for immunization:

• Prefusion conformation stabilization
• Disulfide bonds to lock desired states

Enzyme Engineering

Create thermostable enzyme variants:

• Proline mutations away from active site
• Disulfide bonds in non-catalytic regions

Outputs

stabiliNNator B-factor Scores

Analysis	Score Meaning
proliNNator	Per-residue probability that proline mutation would stabilize
disulfiNNate	Per-cysteine pair probability for engineered disulfide bond

Scores are in the 0-1 range; higher = better candidate for engineering.

Repository Structure

ProteinEngineeringWorkflows/
├── cwl/
│   ├── tools/                        # Individual tool CWL definitions
│   │   ├── boltz.cwl                 # Boltz-2 direct command
│   │   ├── chai.cwl                  # Chai-1 direct command
│   │   ├── stabilinnator.cwl         # Combined stability (dynamic)
│   │   ├── prolinnator.cwl           # Proline analysis (explicit)
│   │   ├── disulfinnate.cwl          # Disulfide analysis (explicit)
│   │   ├── app-boltz.cwl             # App-Boltz.pl wrapper
│   │   ├── app-chai.cwl              # App-ChaiLab.pl wrapper
│   │   ├── app-prolinnator.cwl       # App-StabiliNNator.pl (proline)
│   │   └── app-disulfinnate.cwl      # App-StabiliNNator.pl (disulfide)
│   └── workflows/                    # Combined pipeline workflows
│       ├── protein_stability_pipeline.cwl      # Boltz → stabiliNNator
│       ├── protein_stability_with_chai.cwl     # Chai-1 → stabiliNNator
│       ├── protein_stability_explicit.cwl      # Boltz → prolinnator + disulfinnate
│       ├── protein_stability_explicit_chai.cwl # Chai-1 → prolinnator + disulfinnate
│       ├── protein_stability_app.cwl           # BV-BRC App script workflow (Boltz)
│       └── protein_stability_app_chai.cwl      # BV-BRC App script workflow (Chai-1)
├── examples/
│   ├── crambin_job.yml
│   ├── crambin_fasta_job.yml
│   ├── lysozyme_job.yml
│   └── test_sequences/
├── docs/
│   ├── SCIENTIFIC_RATIONALE.md
│   ├── USER_GUIDE.md
│   └── OUTPUT_INTERPRETATION.md
└── tests/
    └── test_pipeline.sh

Tool Variants

Direct Command Tools

Call the underlying tools directly:

• boltz.cwl → boltz predict
• chai.cwl → chai-lab
• prolinnator.cwl → prolinnator
• disulfinnate.cwl → disulfinnate

BV-BRC App Script Tools

Use BV-BRC application wrappers for infrastructure integration:

• app-boltz.cwl → App-Boltz.pl
• app-chai.cwl → App-ChaiLab.pl
• app-prolinnator.cwl → App-StabiliNNator.pl (proline mode)
• app-disulfinnate.cwl → App-StabiliNNator.pl (disulfide mode)

Requirements

• cwltool >= 3.1
• Docker (for running containerized tools)
• GPU with CUDA support (for structure prediction)
• 64-96 GB RAM (depending on protein size)

License

MIT License