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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 146 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 86 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. 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 44 1

  6. SIFTS SIFTS Public

    Python 43 2

Repositories

Showing 10 of 54 repositories
  • 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 44 Apache-2.0 1 0 0 Updated Nov 13, 2026
  • mmcif-validator Public

    Real-time VSCode extension and standalone Python script for validating mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary.

    PDBeurope/mmcif-validator's past year of commit activity
    Python 11 3 0 0 Updated Nov 12, 2026
  • nf-core-sifts Public
    PDBeurope/nf-core-sifts's past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Nov 11, 2026
  • test-datasets Public Forked from nf-core/test-datasets

    Test data to be used for automated testing with the nf-core pipelines

    PDBeurope/test-datasets's past year of commit activity
    0 MIT 553 0 0 Updated Nov 11, 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 Nov 10, 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 Nov 9, 2026
  • pdbe-data-schemas Public

    Data schemas, examples, and validation tools for integrating partner and community data into PDBe, PDBe-KB, and AlphaFold DB.

    PDBeurope/pdbe-data-schemas's past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Nov 6, 2026
  • SIFTS Public
    PDBeurope/SIFTS's past year of commit activity
    Python 43 2 0 3 Updated Nov 4, 2026
  • nf-core-modules Public Forked from nf-core/modules

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    PDBeurope/nf-core-modules's past year of commit activity
    Nextflow 0 MIT 1,149 0 0 Updated Nov 4, 2026
  • 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 Nov 3, 2026
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