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Monomer database source

Release DOI Monomers Data: CC BY-SA 4.0 Code: AGPL v3

The Peptide Monomer Database is a curated, openly licensed resource for peptide and macrocycle design. 2,488 chemically standardized canonical and non-canonical monomers spanning α/β/γ/δ/ε backbones plus N- and C-terminal caps, with SMILES, InChIKeys, systematic IUPAC names, natural-analogue mapping, computed physicochemical properties (MW, cLogP, tPSA), and commercial-availability signals. Each entry carries a ProteinQure-derived HELM-style monomer shorthand.

This repository is the editable source of truth and build tooling for the ProteinQure monomer database. Data changes belong in data/monomers.json. Output formats are generated and must not be edited by hand.

Interactive Monomer Explorer UI

The Peptide Monomer Database can be interactively browsed, explored and searched via the free Monomer Explorer hosted by ProteinQure. Search the database by name, SMILES, or even a partially remembered name, and retrieve the nearest neighbours of any monomer ranked by Tanimoto similarity. The Chemical Exploration view maps the space around a selected monomer across four regions; close analogues, potential activity cliffs, putative scaffold hops, and the far edge of the space.

Repository roles

Repository Responsibility Accepts changes?
monomer-database-source (this repository) Authoritative JSON, conversion and verification code, tests, and release automation Yes
monomer-database-datasets Versioned output formats intended for download and Zenodo archival No; report changes here

The generated repository is deliberately not an independent data source. Each of its releases corresponds to a release tag in this repository.

Work locally

Install uv and run:

mkdir -p build
install -m 0644 data/monomers.json build/monomers.json
uv run scripts/convert.py --output-type csv data/monomers.json build/monomers.csv
uv run scripts/convert.py --output-type tsv data/monomers.json build/monomers.tsv
uv run scripts/convert.py --output-type sdf data/monomers.json build/monomers.sdf
uv run scripts/verify.py build/monomers.json build/monomers.csv
uv run scripts/verify.py build/monomers.json build/monomers.tsv
uv run scripts/verify.py build/monomers.json build/monomers.sdf
uv run scripts/validate_schema.py data/monomers.json schema/monomers.schema.json
uv run scripts/run_tests.py

The converter requires an explicit --output-type of csv, tsv, or sdf; the destination filename extension does not select conversion behavior. Input must be a non-empty JSON array of objects. Every object must have exactly the same fields; the first object determines column order in tabular formats. Booleans become true or false, null becomes an empty cell, and nested arrays or objects become compact, key-sorted JSON strings.

The SDF output uses each record's SMILES value to create a 2D structure. Its molecule title and rName property are the PQ_SYMBOL, and every JSON field is included as an SD property. RDKit is pinned in the converters' inline PEP 723 metadata so uv run creates the required isolated environment and the generated structure blocks remain reproducible. All outputs use UTF-8 and LF line endings.

Every executable helper declares its third-party dependencies in inline PEP 723 metadata. No persistent virtual environment or requirements file is needed.

The machine-readable field and type contract is schema/monomers.schema.json.

See CONTRIBUTING.md for the data-change workflow and review expectations.

Releases and reproducibility

A published GitHub release with a semantic version tag such as v0.0.1 triggers the release workflow. After tests pass, it:

  1. validates the source JSON against its schema;
  2. builds and verifies every supported output format;
  3. copies the outputs plus the schema into the datasets repository;
  4. generates SHA256SUMS;
  5. commits the generated files to the datasets repository's main branch;
  6. pushes the same immutable tag; and
  7. lets the datasets repository verify the files and create the GitHub release that Zenodo archives.

The exact maintainer setup and release procedure are in RELEASE.md.

Citation and licenses

When using version v1.0.0, cite the archived dataset:

ProteinQure. (2026). Monomer database datasets (Version v1.0.0) [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.21684534

For another version, use the citation and version-specific DOI on its Zenodo record. GitHub-readable citation metadata is provided in CITATION.cff in the monomer-database-datasets repository but the authoritative data source is this monomer-database-source repository.

The data, schema, and documentation are licensed under Creative Commons Attribution-ShareAlike 4.0 International. Executable code, tests, and automation are licensed under the GNU Affero General Public License v3.0 or later. LICENSE-DATA contains a second copy of the data license for explicit downstream reuse. The requested attribution name is ProteinQure. Repository-side Zenodo and GitHub citation metadata are described in ZENODO.md in the monomer-database-datasets repository.