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@Steinbeck-Lab

Steinbeck-Lab

Official GitHub organization for the Steinbeck group Jena, Germany
README.md

Steinbeck Lab: open software for chemistry and natural products, Natural Products Cheminformatics, Friedrich Schiller University Jena

cheminf.uni-jena.de naturalproducts.net All repositories

This organisation hosts the research software of the Steinbeck Lab at Friedrich Schiller University Jena. Open science, open source, open data.

COCONUT, the COlleCtion of Open Natural prodUcTs: deposit, curate and reuse natural product data. A specimen cabinet: an index card with menthol passes the ChEMBL curation stamp, is filed, and its drawer CNP0243697 slides out with menthol's stereo variants. DECIMER.ai: extract chemical structures from PDFs and images, and turn them into SMILES. A scanner and typewriter: a scan head passes over a printed page, a cutting die lifts out the structure drawing, a flag marks it as a structure, and a typewriter types its SMILES on tape. ChemAudit: validate, standardize and score chemical structures before they feed a model or a database. An inspection line: aspirin's sodium salt scores 85, a suction arm strips the sodium, and the parent acid scores 100. Cheminformatics Microservice: CDK, RDKit and Open Babel, unified behind one REST API and web app. A switchboard: one request plug is patched into the CDK, RDKit or Open Babel jack, and the display shows that toolkit's canonical SMILES for caffeine. MORTAR, the MOlecule fRagmenTAtion fRamework: in silico fragmentation on the desktop. A fragmentation workstation: a magazine feeds molecules from a set, a turret runs a two-die pipeline (Sugar Removal Utility, then Scaffold Generator), fragments sort into a histogram rack beside the Overview and Items views, and a printer exports the results as CSV, PDB, PDF or SDF. Orthonym: deterministic structure-to-IUPAC names, each checked by an OPSIN round trip. A typewriter and proofreader: a name is typed on a card, OPSIN reads it back into a structure, a comparator checks the match, and a stamp prints the tier. SURGE: a fast open-source chemical graph generator for every isomer of a formula. An isomer counter: each turn of the crank clicks the wheels on and prints the next of the 7 constitutional isomers of C4H10O, never a duplicate. Sherlock: computer-assisted structure elucidation, from NMR spectra to structures. A chart recorder and balance: the pen climbs the eight 13C peaks of caffeine, and a balance ranks candidate structures by how well their predicted shifts match.

Code and papers

Project Source Paper
COCONUT Steinbeck-Lab/coconut stars Nucleic Acids Research, 2025
DECIMER.ai Steinbeck-Lab/DECIMER.ai, Image Transformer stars Nature Communications, 2023
ChemAudit Kohulan/ChemAudit stars Zenodo
Cheminformatics Microservice Steinbeck-Lab/cheminformatics-microservice stars Journal of Cheminformatics, 2023
MORTAR FelixBaensch/MORTAR stars Journal of Cheminformatics, 2022
Orthonym Steinbeck-Lab/Orthonym, Orthonym-Web stars
SURGE StructureGenerator/surge stars Journal of Cheminformatics, 2022
Sherlock Steinbeck-Lab/sherlock stars Molecules, 2023

More from the lab: STOUT (SMILES to IUPAC names), CIDER (chemical dataset comparison), and everything else.

Built on CDK, RDKit, Open Babel and OPSIN, in Python, Java, C, PHP and TypeScript, shipped with Docker. The machines are drawn with Anatomy.

Brewed in Jena since 1997

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  1. coconut coconut Public

    COCONUT (COlleCtion of Open Natural prodUcTs): A comprehensive platform facilitating natural product research by providing data, tools, and services for deposition, curation, and reuse.

    PHP 69 5

  2. cheminformatics-microservice cheminformatics-microservice Public

    This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

    Python 73 10

  3. DECIMER-Image_Transformer DECIMER-Image_Transformer Public

    Forked from Kohulan/DECIMER-Image_Transformer

    DECIMER Image Transformer is a deep-learning-based tool designed for automated recognition of chemical structure images. Leveraging transformer architectures, the model converts chemical images int…

    Python 1

  4. MORTAR MORTAR Public

    Forked from FelixBaensch/MORTAR

    MOlecule fRagmenTAtion fRamework

    Java

  5. surge surge Public

    Forked from StructureGenerator/surge

    A Fast Chemical Graph Generator

    C 1

  6. Orthonym Orthonym Public

    Deterministic structure-to-IUPAC-name generator. Names are checked by an OPSIN round trip, the engine declines rather than guess, and --provenance says how each name was checked.

    Python 15 3

Repositories

Showing 10 of 53 repositories
  • Orthonym Public

    Deterministic structure-to-IUPAC-name generator. Names are checked by an OPSIN round trip, the engine declines rather than guess, and --provenance says how each name was checked.

    Steinbeck-Lab/Orthonym's past year of commit activity
    Python 15 MIT 3 1 2 Updated Oct 31, 2026
  • .github Public
    Steinbeck-Lab/.github's past year of commit activity
    Python 0 0 0 0 Updated Oct 30, 2026
  • DECIMER.ai Public

    DECIMER.ai: extract chemical structures from PDFs and images, and turn them into SMILES

    Steinbeck-Lab/DECIMER.ai's past year of commit activity
    Python 2 MIT 0 4 1 Updated Oct 28, 2026
  • DECIMER-Image_Transformer Public Forked from Kohulan/DECIMER-Image_Transformer

    DECIMER Image Transformer is a deep-learning-based tool designed for automated recognition of chemical structure images. Leveraging transformer architectures, the model converts chemical images into SMILES strings, enabling the digitization of chemical data from scanned documents, literature, and patents.

    Steinbeck-Lab/DECIMER-Image_Transformer's past year of commit activity
    Python 1 MIT 81 0 1 Updated Oct 28, 2026
  • DECIMER.ai-legacy Public archive Forked from OBrink/DECIMER.ai

    Archived: the original Laravel 8 version of decimer.ai. The site now runs from Steinbeck-Lab/DECIMER.ai.

    Steinbeck-Lab/DECIMER.ai-legacy's past year of commit activity
    PHP 84 MIT 19 0 0 Updated Oct 28, 2026
  • Orthonym-Web Public

    Web app for the Orthonym engine: draw or paste a structure, get its IUPAC name. OPSIN reads every name back, and each name shows the tier it earned: PIN, fallback, best effort, or no name.

    Steinbeck-Lab/Orthonym-Web's past year of commit activity
    Python 3 MIT 0 1 1 Updated Oct 27, 2026
  • kladde_Digifellows Public

    Learning materials for SciPeaks ELN for OC-Praktikum

    Steinbeck-Lab/kladde_Digifellows's past year of commit activity
    CSS 0 0 0 0 Updated Oct 26, 2026
  • cheminformatics-microservice Public

    This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

    Steinbeck-Lab/cheminformatics-microservice's past year of commit activity
    Python 73 MIT 10 1 0 Updated Oct 25, 2026
  • coconut Public

    COCONUT (COlleCtion of Open Natural prodUcTs): A comprehensive platform facilitating natural product research by providing data, tools, and services for deposition, curation, and reuse.

    Steinbeck-Lab/coconut's past year of commit activity
    PHP 69 5 75 4 Updated Oct 22, 2026
  • DECIMER-Image-Segmentation Public Forked from Kohulan/DECIMER-Image-Segmentation

    https://decimer.ai

    Steinbeck-Lab/DECIMER-Image-Segmentation's past year of commit activity
    Jupyter Notebook 0 MIT 38 0 0 Updated Jan 28, 2026
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