BoltzYML

Preprocessing-file generator for ternary (Protein 1 + Ligand + Protein 2) binding prediction with Boltz-2.

Live web app →  ·  CLI  ·  How it works

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When to use BoltzYML

Use this tool only if you want to study how the interaction between two proteins changes in the presence of a ligand.

That is the one scenario it is built for: a small molecule sits in a pocket of Protein 1, and you want Boltz-2 to predict how Protein 1 and Protein 2 dock together while that ligand is bound (or absent, as a control). Typical use cases:

• ABA signaling: PYR/PYL/RCAR receptor + ABA + PP2C phosphatase
• Allosteric drug screens where a ligand is expected to enable or block partner binding
• Any ternary system where the ligand sits on Protein 1 and you care about the Protein 1 ↔ Protein 2 interface

If your problem is just protein–protein docking, just protein–ligand docking, or anything that is not a ternary Protein 1 + Ligand + Protein 2 complex, BoltzYML will not help — write the YAML directly or use the Boltz-2 examples.

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What it does

You hand BoltzYML two CIF files:

Input	Contents	Role
protein1_ligand.cif	Protein 1 bound to the ligand (docked structure, e.g. AlphaFill, Glide, AutoDock)	Source of Protein 1 sequence + ligand identity + pocket residues
protein1_protein2.cif	Protein 1 together with Protein 2 (e.g. AlphaFold3 prediction)	Source of Protein 2 sequence

BoltzYML then runs entirely in your browser (or via the CLI) and produces a single Boltz-2 v1 YAML with:

1. Protein 1 sequence on chain A
2. The ligand on chain B (with its PDB CCD code)
3. Protein 2 sequence on chain C
4. A pocket constraint listing the Protein 1 CA atoms within a cutoff of the ligand
5. An affinity property block targeting the ligand

That YAML is then fed straight into the Boltz-2 CLI.

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Two ways to run it

1. Web app (recommended)

Open https://ayushmania2002.github.io/boltzyml/, drop in the two CIFs, click Generate YAML, download the file.

Everything happens in your browser — no uploads, no server, no telemetry. Works on any modern browser, no installation required.

2. Command-line interface

Install from PyPI:

pip install boltzyml

Then run:

boltzyml \
    --ligand   PYL2_ABA.cif \
    --complex  PYL2_PP2C30.cif \
    --output   PYL2_ABA_PP2C30.yaml

Pure Python 3.10+, zero runtime dependencies (no gemmi, no numpy, no pyyaml required).

You can also clone the repo and run it as a module without installing:

git clone https://github.com/Ayushmania2002/boltzyml.git
cd boltzyml
pip install -e .
boltzyml --ligand A.cif --complex B.cif -o out.yaml

CLI options

Flag	Description	Default
--ligand	CIF with Protein 1 + Ligand	required
--complex	CIF with Protein 1 + Protein 2	required
-o, --output	Output YAML path	{ligand-stem}__{complex-stem}.yaml
--job-name	Job name used for the default output filename	derived
--cutoff	CA-to-ligand distance cutoff in Å	6.0
--ccd	Override the ligand CCD code (used verbatim in the YAML's ccd: field)	auto-detect
--no-affinity	Skip the affinity prediction block	off
--no-pocket	Skip the pocket constraints block	off
--no-force	Emit force: false on the pocket block	off
-v, --verbose	Print detected chains, ligand, and contacts	off

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How it works

1. Parse both CIFs. The parser handles two layouts seen in the wild: single-line atom records (AlphaFold3 style, 18 fields per line) and two-line records (some AlphaFill outputs, 21 fields split 17 + 4).
2. Identify the ligand. The first non-water HETATM whose comp ID is not a standard amino acid is taken as the ligand. If the CIF labels it generically (LIG, UNL, UNK), the tool warns and asks for a CCD override.
3. Assign chains. Protein 1 = the longest protein chain in the ligand CIF. The corresponding chain in the complex CIF is matched by 5-mer overlap similarity; the remaining chain is Protein 2.
4. Compute pocket contacts. CA atoms of Protein 1 within --cutoff Å of any ligand atom are emitted as [A, residue_number] entries, using the CIF's auth_seq_id so the numbers match Boltz-2's own residue numbering.
5. Emit YAML. A deterministic Boltz-2 v1 YAML is written out, in the field order Boltz-2 expects.

Why CA-only at 6 Å? CA-to-ligand at 6 Å approximates all-atom contacts at ~4 Å, which is the right scale for the soft pocket constraint Boltz-2 applies as an inference-time potential.

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Example output

version: 1
sequences:
  - protein:
      id: A
      sequence: MEAHVERALREGLTEEERAALEPAVMAHHTFPPSTTTATTAAATCTSLVTQRVAAPVRAVWPIVRSFGNPQRYKHFVRTCALAAGDGASVGSVREVTVVSGLPASTSTERLEMLDDDRHIISFRVVGGQHRLRNYRSVTSVTEFQPPAAGPAPAPPYCVVVESYVVDVPDGNTAEDTRMFTDTVVKLNLQKLAAVAEDSSSASRRRD
  - ligand:
      id: B
      ccd: A8S
  - protein:
      id: C
      sequence: MAEICCEVVAGSSSEGKGPECDTGSRAARRRR...
constraints:
  - pocket:
      binder: B
      contacts:
        - [A, 76]    # PHE76
        - [A, 98]    # VAL98
        - [A, 103]   # PRO103
        - [A, 104]   # ALA104
        - [A, 107]   # SER107
        - [A, 130]   # HIS130
        - [A, 131]   # ARG131
        - [A, 132]   # LEU132
        - [A, 181]   # THR181
        - [A, 184]   # VAL184
        - [A, 185]   # VAL185
      max_distance: 6.0
      force: true
properties:
  - affinity:
      binder: B

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Running Boltz-2 on the output

pip install boltz

boltz predict job.yaml \
    --use_msa_server \
    --use_potentials \
    --diffusion_samples 3 \
    --recycling_steps  3 \
    --step_scale       1.638

Key result files:

File	Contents
*_model_0.pdb	Predicted ternary structure
confidence_*.json	iptm, ptm, ligand_iptm
affinity_*.json	affinity_pred_value in kcal/mol
pae_*.npz	Predicted aligned error matrix

Sanity checks:

• iptm > 0.6 — confident protein–protein interface
• ligand_iptm > 0.5 — confident ligand placement
• A low off-diagonal block between chain A and chain C in the PAE map = confident interaction

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Project layout

boltzyml/
├── index.html              # Web app (deploy to GitHub Pages as-is)
├── logo.png                # Wordmark — favicon + header logo
├── banner.png              # Pipeline schematic — used in this README
│
├── pyproject.toml          # PyPI packaging metadata (hatchling)
├── LICENSE                 # MIT
│
├── src/boltzyml/
│   ├── __init__.py         # Public API re-exports
│   ├── cli.py              # CLI entry point (boltzyml command)
│   ├── parser.py           # CIF parser (1-line and 2-line layouts)
│   ├── contacts.py         # CA-to-ligand pocket contact computation
│   ├── utils.py            # Chain assignment via k-mer similarity
│   └── yaml_writer.py      # Boltz-2 v1 YAML emitter
│
└── tests/
    ├── test_parser.py      # Synthetic CIFs for both layouts
    ├── test_contacts.py    # Cutoff filtering, missing ligand, chain remap
    └── test_cli.py         # End-to-end CLI smoke test

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Tests

pip install -e ".[dev]"
pytest

Or run each file directly without pytest:

python tests/test_parser.py
python tests/test_contacts.py
python tests/test_cli.py

Each script exits non-zero on failure and prints all tests passed otherwise.

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Gotchas

• LIG / UNL / UNK ligands. Docking tools often name the ligand generically. The real PDB CCD code (e.g. A8S for abscisic acid, ATP, HEM) belongs in the ccd: field — use the CCD override in the web app or --ccd on the CLI. Verify codes at https://www.rcsb.org/ligand/.
• Residue numbering. Boltz-2 uses auth_seq_id from your CIF. If your CIF starts at residue 14 (truncated structure), the pocket numbers will start at 14 too — that is correct.
• Apo vs holo Protein 1. For the ligand CIF, use the holo (ligand-bound) structure, not the apo AlphaFold prediction, so the pocket is in the right conformation.
• Tamarind Bio users. The same YAML works on https://app.tamarind.bio/boltz. Do not include a templates: block when submitting there — use Tamarind's UI fields for template CIFs instead.

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Citation

If you use BoltzYML in published or shared work, please cite both of the following.

1. BoltzYML (this tool):

Mallick, A. BoltzYML: a preprocessing-file generator for Boltz-2 ternary (Protein 1 + Ligand + Protein 2) binding prediction. Zenodo (2026). https://doi.org/10.5281/zenodo.20397272

BibTeX:

@software{boltzyml_2026,
  author    = {Mallick, Ayushman},
  title     = {{BoltzYML}: a preprocessing-file generator for Boltz-2 ternary
               (Protein 1 + Ligand + Protein 2) binding prediction},
  year      = {2026},
  publisher = {Zenodo},
  version   = {1.0.0},
  doi       = {10.5281/zenodo.20397272},
  url       = {https://doi.org/10.5281/zenodo.20397272}
}

2. Boltz-2 (the upstream model BoltzYML produces input for):

Wohlwend, J. et al. Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction. 2024. https://github.com/jwohlwend/boltz

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License

MIT. Copyright © 2026 Ayushman Mallick.