Repositories list

• deposition-toolkit

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

  Python

  •00 forks in PDBeurope/deposition-toolkit•00 stars in PDBeurope/deposition-toolkit•00 issues in PDBeurope/deposition-toolkit•00 pull requests in PDBeurope/deposition-toolkit•Updated Nov 14, 2026Nov 14, 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 A…

  pythonbioinformaticsstructural-biology+ 7

  pythonbioinformaticsstructural-biologymcpapi-serverknowledge-graphpdbeprotein-structuresllm-toolsai-integration

  Python

  •

  Apache License 2.0

  •11 fork in PDBeurope/PDBe-MCP-Servers•4444 stars in PDBeurope/PDBe-MCP-Servers•00 issues in PDBeurope/PDBe-MCP-Servers•00 pull requests in PDBeurope/PDBe-MCP-Servers•Updated Nov 14, 2026Nov 14, 2026

• ner_for_protein_structures

  Public
  Python

  •

  Other

  •00 forks in PDBeurope/ner_for_protein_structures•11 star in PDBeurope/ner_for_protein_structures•00 issues in PDBeurope/ner_for_protein_structures•11 pull request in PDBeurope/ner_for_protein_structures•Updated Nov 13, 2026Nov 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.

  pythonbioinformaticsdata-validation+ 6

  pythonbioinformaticsdata-validationstructural-biologypdbschema-validationcifmmcifscientific-data

  Python

  •33 forks in PDBeurope/mmcif-validator•1111 stars in PDBeurope/mmcif-validator•22 issues in PDBeurope/mmcif-validator•00 pull requests in PDBeurope/mmcif-validator•Updated Nov 13, 2026Nov 13, 2026

• nf-core-sifts

  Public
  Nextflow

  •

  MIT License

  •00 forks in PDBeurope/nf-core-sifts•00 stars in PDBeurope/nf-core-sifts•00 issues in PDBeurope/nf-core-sifts•00 pull requests in PDBeurope/nf-core-sifts•Updated Nov 11, 2026Nov 11, 2026

• test-datasets

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

  MIT License

  •554554 forks in PDBeurope/test-datasets•00 stars in PDBeurope/test-datasets•00 issues in PDBeurope/test-datasets•00 pull requests in PDBeurope/test-datasets•Updated Nov 11, 2026Nov 11, 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.

  C++

  •

  Creative Commons Zero v1.0 Universal

  •11 fork in PDBeurope/AFDB-Integration-Kit•33 stars in PDBeurope/AFDB-Integration-Kit•11 issue in PDBeurope/AFDB-Integration-Kit•22 pull requests in PDBeurope/AFDB-Integration-Kit•Updated Nov 9, 2026Nov 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.

  Python

  •

  Apache License 2.0

  •00 forks in PDBeurope/pdbe-data-schemas•00 stars in PDBeurope/pdbe-data-schemas•00 issues in PDBeurope/pdbe-data-schemas•00 pull requests in PDBeurope/pdbe-data-schemas•Updated Nov 6, 2026Nov 6, 2026

• SIFTS

  Public
  Python

  •

  Other

  •22 forks in PDBeurope/SIFTS•4343 stars in PDBeurope/SIFTS•00 issues in PDBeurope/SIFTS•33 pull requests in PDBeurope/SIFTS•Updated Nov 4, 2026Nov 4, 2026

• nf-core-modules

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

  Nextflow

  •

  MIT License

  •1.1k1.1k forks in PDBeurope/nf-core-modules•00 stars in PDBeurope/nf-core-modules•00 issues in PDBeurope/nf-core-modules•00 pull requests in PDBeurope/nf-core-modules•Updated Nov 4, 2026Nov 4, 2026

• heatmap-component

  Public
  Canvas-based Interactive Heatmap Component

  TypeScript

  •

  Apache License 2.0

  •00 forks in PDBeurope/heatmap-component•22 stars in PDBeurope/heatmap-component•00 issues in PDBeurope/heatmap-component•11 pull request in PDBeurope/heatmap-component•Updated Nov 3, 2026Nov 3, 2026

• InsightFold

  Public
  Notebook-Driven Development to nurture new features supported and maintained by our diverse user base.

  Python

  •11 fork in PDBeurope/InsightFold•11 star in PDBeurope/InsightFold•00 issues in PDBeurope/InsightFold•55 pull requests in PDBeurope/InsightFold•Updated Oct 30, 2026Oct 30, 2026

• rellig

  Public
  Identifies relevant ligands in the PDB

  pythonbioinformaticscheminformatics+ 6

  pythonbioinformaticscheminformaticsstructural-biologypdbdrug-discoverymmcifligandsprotein-ligand

  Python

  •

  Apache License 2.0

  •00 forks in PDBeurope/rellig•1010 stars in PDBeurope/rellig•11 issue in PDBeurope/rellig•33 pull requests in PDBeurope/rellig•Updated Oct 30, 2026Oct 30, 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

  Jupyter Notebook

  •

  Apache License 2.0

  •11 fork in PDBeurope/IUCr-annotation-pipeline•00 stars in PDBeurope/IUCr-annotation-pipeline•00 issues in PDBeurope/IUCr-annotation-pipeline•11 pull request in PDBeurope/IUCr-annotation-pipeline•Updated Oct 27, 2026Oct 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

  pythonbioinformaticscheminformatics+ 7

  pythonbioinformaticscheminformaticsstructural-biologypdbrdkitmmcifligandschemical-databasechemical-components

  Python

  •

  Apache License 2.0

  •1212 forks in PDBeurope/ccdutils•8686 stars in PDBeurope/ccdutils•00 issues in PDBeurope/ccdutils•22 pull requests in PDBeurope/ccdutils•Updated Oct 26, 2026Oct 26, 2026

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •4.2k4.2k forks in PDBeurope/bioconda-recipes•00 stars in PDBeurope/bioconda-recipes•00 issues in PDBeurope/bioconda-recipes•00 pull requests in PDBeurope/bioconda-recipes•Updated Oct 24, 2026Oct 24, 2026

• mmcif-gen

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

  pythonbioinformaticsstructural-biology+ 6

  pythonbioinformaticsstructural-biologypdbprotein-data-bankdata-generationmmcifscientific-datacif-format

  Python

  •11 fork in PDBeurope/mmcif-gen•77 stars in PDBeurope/mmcif-gen•22 issues in PDBeurope/mmcif-gen•22 pull requests in PDBeurope/mmcif-gen•Updated Oct 24, 2026Oct 24, 2026

• mmcif-metadata-import

  Public
  Import metadata from mmCIF files into metadata-only files, or merge them into existing models

  Python

  •

  Apache License 2.0

  •11 fork in PDBeurope/mmcif-metadata-import•33 stars in PDBeurope/mmcif-metadata-import•00 issues in PDBeurope/mmcif-metadata-import•00 pull requests in PDBeurope/mmcif-metadata-import•Updated Oct 21, 2026Oct 21, 2026

• protvista-pdb

  Public
  PDB ProtVista Viewer

  JavaScript

  •

  Apache License 2.0

  •88 forks in PDBeurope/protvista-pdb•1111 stars in PDBeurope/protvista-pdb•00 issues in PDBeurope/protvista-pdb•1212 pull requests in PDBeurope/protvista-pdb•Updated Oct 16, 2026Oct 16, 2026

• pdb-topology-viewer

  Public
  PDB Topology Viewer

  TypeScript

  •

  Apache License 2.0

  •55 forks in PDBeurope/pdb-topology-viewer•77 stars in PDBeurope/pdb-topology-viewer•11 issue in PDBeurope/pdb-topology-viewer•1616 pull requests in PDBeurope/pdb-topology-viewer•Updated Oct 16, 2026Oct 16, 2026

• pdb-rna-viewer

  Public
  The PDB RNA viewer depicts the secondary structure of a RNA in a 2D representation

  visualizationbioinformaticstypescript+ 5

  visualizationbioinformaticstypescriptstructural-biologypdbrna-structurernamolecular-visualization

  TypeScript

  •

  Other

  •33 forks in PDBeurope/pdb-rna-viewer•44 stars in PDBeurope/pdb-rna-viewer•22 issues in PDBeurope/pdb-rna-viewer•1212 pull requests in PDBeurope/pdb-rna-viewer•Updated Oct 16, 2026Oct 16, 2026

• ligand-env

  Public
  Public repository of the PDBe ligand environment component

  visualizationbioinformaticstypescript+ 6

  visualizationbioinformaticstypescriptstructural-biologypdbdrug-discoveryprotein-ligandmolecular-interactionsligand-interactions

  TypeScript

  •

  Apache License 2.0

  •00 forks in PDBeurope/ligand-env•66 stars in PDBeurope/ligand-env•00 issues in PDBeurope/ligand-env•99 pull requests in PDBeurope/ligand-env•Updated Oct 16, 2026Oct 16, 2026

• protein-cluster-conformers

  Public
  Clusters protein chains based on CA distance difference

  pythonbioinformaticsstructural-biology+ 6

  pythonbioinformaticsstructural-biologycomputational-biologystructural-analysisprotein-clusteringdistance-matrixprotein-structuresprotein-conformation

  Python

  •

  Other

  •11 fork in PDBeurope/protein-cluster-conformers•1919 stars in PDBeurope/protein-cluster-conformers•11 issue in PDBeurope/protein-cluster-conformers•66 pull requests in PDBeurope/protein-cluster-conformers•Updated Oct 9, 2026Oct 9, 2026

• BioSolr

  Public
  A project aiming "to significantly advance the state of the art with regard to indexing and querying biomedical data with freely available open source software"

  Java

  •

  Apache License 2.0

  •2929 forks in PDBeurope/BioSolr•00 stars in PDBeurope/BioSolr•00 issues in PDBeurope/BioSolr•11 pull request in PDBeurope/BioSolr•Updated Sep 17, 2026Sep 17, 2026

• pdb-3d-complex

  Public
  Summary web-component for the PDB 3D complex, a server that analyses the complexes in crystal structures

  TypeScript

  •

  Apache License 2.0

  •11 fork in PDBeurope/pdb-3d-complex•33 stars in PDBeurope/pdb-3d-complex•00 issues in PDBeurope/pdb-3d-complex•66 pull requests in PDBeurope/pdb-3d-complex•Updated Sep 11, 2026Sep 11, 2026

• surface-calculator

  Public
  TypeScript

  •

  Apache License 2.0

  •00 forks in PDBeurope/surface-calculator•11 star in PDBeurope/surface-calculator•00 issues in PDBeurope/surface-calculator•88 pull requests in PDBeurope/surface-calculator•Updated Sep 3, 2026Sep 3, 2026

• pdb-images

  Public
  Generates images from mmCIF/BCIF files

  bioinformaticstypescriptstructural-biology+ 6

  bioinformaticstypescriptstructural-biologypdbmolecular-structuresmolecular-graphicsmmcif3d-visualizationprotein-visualization

  TypeScript

  •

  Apache License 2.0

  •55 forks in PDBeurope/pdb-images•4646 stars in PDBeurope/pdb-images•00 issues in PDBeurope/pdb-images•88 pull requests in PDBeurope/pdb-images•Updated Sep 3, 2026Sep 3, 2026

• pdbe-notebooks

  Public
  pythonbioinformaticsstructural-biology+ 6

  pythonbioinformaticsstructural-biologypdbscientific-computingdata-analysisjupyter-notebookspdbeprotein-structures

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks in PDBeurope/pdbe-notebooks•11 star in PDBeurope/pdbe-notebooks•00 issues in PDBeurope/pdbe-notebooks•00 pull requests in PDBeurope/pdbe-notebooks•Updated Aug 27, 2026Aug 27, 2026

• pdb-residue-interactions

  Public
  Residue contacts viewer in Protein Contacts Atlas

  TypeScript

  •00 forks in PDBeurope/pdb-residue-interactions•22 stars in PDBeurope/pdb-residue-interactions•00 issues in PDBeurope/pdb-residue-interactions•99 pull requests in PDBeurope/pdb-residue-interactions•Updated Aug 10, 2026Aug 10, 2026

• pdbe-api-training

  Public
  Interactive Python notebooks for PDBe API training

  pythonbioinformaticsstructural-biology+ 7

  pythonbioinformaticsstructural-biologypdbrest-apijupyter-notebookstraining-materialsdata-accesspdbeapi-tutorial

  Jupyter Notebook

  •

  Other

  •2121 forks in PDBeurope/pdbe-api-training•6262 stars in PDBeurope/pdbe-api-training•44 issues in PDBeurope/pdbe-api-training•11 pull request in PDBeurope/pdbe-api-training•Updated Jun 22, 2026Jun 22, 2026