Monomer database datasets

The 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 contains versioned output formats for the monomer database. The files are generated from the authoritative monomer-database-source repository and are available for download and archival through Zenodo. ProteinQure is identified as the organizational creator; see ZENODO.md.

Interactive Monomer Explorer UI

The 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.

Download and verify

For reproducible work, use a tagged GitHub release or its corresponding Zenodo version rather than main. Generated artifacts are kept under data/ so they remain separate from repository administration and documentation. Each release contains:

• data/monomers.json — the generated structured representation for that version;
• data/monomers.csv — a deterministic tabular conversion;
• data/monomers.tsv — the equivalent tab-separated conversion;
• data/monomers.sdf — an SD file containing 2D structures and all JSON fields as molecule properties;
• data/monomers.schema.json — the JSON Schema for the structured data; and
• data/SHA256SUMS — checksums for all five dataset artifacts.

After downloading all six files, checksums can be verified without additional software:

cd data
sha256sum --check SHA256SUMS

JSON records have a consistent set of fields. Tabular columns follow the key order of the first JSON record. UTF-8 text and LF line endings are used throughout.

For full validation, place the six files under data/ in a checkout of this repository and run uv run scripts/verify_release.py data. The verifier reconstructs CSV, TSV, and SDF from the JSON source, compares their bytes, validates the JSON Schema, and verifies SHA256SUMS. Its dependencies are declared in inline PEP 723 metadata. Run its tests with uv run scripts/run_tests.py.

Provenance and versioning

Every datasets release is created from the identically tagged source release. For example, datasets tag v0.0.1 is derived from source tag v0.0.1. The source workflow performs the conversion; this repository independently reconstructs each generated output format, compares it byte-for-byte, verifies the checksums, and then creates the datasets GitHub release.

main may advance after a release. A tag, GitHub release, or version-specific Zenodo DOI identifies an immutable snapshot.

The latest archived dataset is available from the Zenodo record for all versions. Version v1.0.0 is permanently available at doi:10.5281/zenodo.21684534.

Corrections and contributions

Do not directly edit generated files or propose data changes in this repository. Report problems and propose data, schema, tooling, or documentation changes in ProteinQure/monomer-database-source. Include the affected record identifiers and version or DOI. See CONTRIBUTING.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, and the authoritative data source is the monomer-database-source repository.

The dataset, schema, and documentation are licensed under Creative Commons Attribution-ShareAlike 4.0 International. The requested attribution name is ProteinQure. Repository automation is licensed under the GNU Affero General Public License v3.0 or later. Repository-side Zenodo and GitHub citation metadata are described in ZENODO.md.