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@PDBeurope

PDBe EMBL-EBI

Engineering at @PDBeurope : building open-source tools, APIs and data infrastructure for structural biology. Part of @embl-ebi.

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  1. arpeggio arpeggio Public

    Calculation of interatomic interactions in molecular structures

    Python 145 25

  2. ccdutils ccdutils Public

    A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

    Python 85 12

  3. pdbe-api-training pdbe-api-training Public

    Interactive Python notebooks for PDBe API training

    Jupyter Notebook 62 21

  4. pdb-images pdb-images Public

    Generates images from mmCIF/BCIF files

    TypeScript 46 5

  5. SIFTS SIFTS Public

    Python 43 2

  6. PDBe-MCP-Servers PDBe-MCP-Servers Public

    PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema as…

    Python 43 1

Repositories

Showing 10 of 53 repositories
  • heatmap-component Public

    Canvas-based Interactive Heatmap Component

    PDBeurope/heatmap-component's past year of commit activity
    TypeScript 2 Apache-2.0 0 0 1 Updated Oct 29, 2026
  • SIFTS Public
    PDBeurope/SIFTS's past year of commit activity
    Python 43 2 0 4 Updated Oct 29, 2026
  • deposition-toolkit Public

    Set of tools to help prepare files, generate CCDs, create report for a deposition for OneDep deposition

    PDBeurope/deposition-toolkit's past year of commit activity
    Python 0 0 0 0 Updated Oct 28, 2026
  • ner_for_protein_structures Public
    PDBeurope/ner_for_protein_structures's past year of commit activity
    Python 1 0 0 0 Updated Oct 27, 2026
  • IUCr-annotation-pipeline Public

    A Python-based pipeline to wrap around a transformer model to annotated IUCr-style JATS XML for functional protein residues

    PDBeurope/IUCr-annotation-pipeline's past year of commit activity
    Jupyter Notebook 0 Apache-2.0 1 0 1 Updated Oct 27, 2026
  • PDBe-MCP-Servers Public

    PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

    PDBeurope/PDBe-MCP-Servers's past year of commit activity
    Python 43 Apache-2.0 1 0 1 Updated Oct 27, 2026
  • ccdutils Public

    A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

    PDBeurope/ccdutils's past year of commit activity
    Python 85 Apache-2.0 12 0 2 Updated Oct 26, 2026
  • AFDB-Integration-Kit Public

    This repository provides a set of easy-to-use tools for generating the required files and metadata to seamlessly integrate your models into AFDB.

    PDBeurope/AFDB-Integration-Kit's past year of commit activity
    C++ 3 CC0-1.0 1 1 2 Updated Oct 26, 2026
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    PDBeurope/bioconda-recipes's past year of commit activity
    Shell 0 MIT 4,205 0 0 Updated Oct 24, 2026
  • mmcif-gen Public

    This application is designed to create mmcif files from facilities data.

    PDBeurope/mmcif-gen's past year of commit activity
    Python 7 1 2 2 Updated Oct 24, 2026
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