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PDBe EMBL-EBI

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  1. arpeggio arpeggio Public

    Calculation of interatomic interactions in molecular structures

    Python 117 23

  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 74 12

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

    Interactive Python notebooks for PDBe API training

    Jupyter Notebook 58 21

  4. pdb-images pdb-images Public

    Generates images from mmCIF/BCIF files

    TypeScript 44 5

  5. pdbecif pdbecif Public

    A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB"

    Python 38 4

  6. protein-cluster-conformers protein-cluster-conformers Public

    Clusters protein chains based on CA distance difference

    Python 16 1

Repositories

Showing 10 of 44 repositories
  • pdbe-api-training Public

    Interactive Python notebooks for PDBe API training

    PDBeurope/pdbe-api-training’s past year of commit activity
    Jupyter Notebook 58 21 0 3 Updated Jan 8, 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 4 0 0 0 Updated Dec 17, 2025
  • surface-calculator Public
    PDBeurope/surface-calculator’s past year of commit activity
    TypeScript 1 Apache-2.0 0 0 0 Updated Dec 15, 2025
  • 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 0 Updated Dec 12, 2025
  • 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 3 Apache-2.0 0 0 0 Updated Dec 4, 2025
  • pdbe-notebooks Public
    PDBeurope/pdbe-notebooks’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Nov 28, 2025
  • afdb-notebooks Public
    PDBeurope/afdb-notebooks’s past year of commit activity
    Jupyter Notebook 1 CC0-1.0 0 0 0 Updated Nov 11, 2025
  • rellig Public

    Identifies relevant ligands in the PDB

    PDBeurope/rellig’s past year of commit activity
    Python 9 Apache-2.0 0 1 1 Updated Oct 20, 2025
  • 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 74 Apache-2.0 12 2 1 Updated Oct 15, 2025
  • ligand-env Public

    Public repository of the PDBe ligand environment component

    PDBeurope/ligand-env’s past year of commit activity
    TypeScript 3 Apache-2.0 0 2 0 Updated Oct 15, 2025
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