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@PDBeurope PDBe EMBL-EBI

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    42 repositories

    • pdbe-api-training

      Public
      Interactive Python notebooks for PDBe API training
      Jupyter Notebook
      •
      Other
      •20•54•0•3•Updated Jun 19, 2025Jun 19, 2025

    • pdb-images

      Public
      Generates images from mmCIF/BCIF files
      TypeScript
      •
      Apache License 2.0
      •4•40•0•0•Updated Jun 12, 2025Jun 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.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • Investigations

      Public
      This application is designed to create mmcif files from facilities data.
      Python
      •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • InvestigationCIF

      Public
      Documentation for the mmcif Investigation dictionary
      structural-biologymmcif
      Creative Commons Zero v1.0 Universal
      •1•1•0•0•Updated May 23, 2025May 23, 2025

    • surface-calculator

      Public
      TypeScript
      •
      Apache License 2.0
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • surface-calculator-x

      Public
      TypeScript
      •0•1•0•0•Updated Apr 14, 2025Apr 14, 2025

    • 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
      •27•0•0•0•Updated Apr 2, 2025Apr 2, 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
      Python
      •
      Apache License 2.0
      •8•57•2•1•Updated Mar 6, 2025Mar 6, 2025

    • protein-cluster-conformers

      Public
      Clusters protein chains based on CA distance difference
      bioinformaticsclusteringproteinsstructural-biologypdbprotein-structuresuperpositionstructural-bioinformaticsconformal-predictionbioinformatics-tool
      Python
      •
      Other
      •0•14•0•1•Updated Feb 4, 2025Feb 4, 2025

    • pdbe-notebooks

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • heatmap-component

      Public
      Canvas-based Interactive Heatmap Component
      TypeScript
      •
      Apache License 2.0
      •0•2•0•0•Updated Dec 19, 2024Dec 19, 2024

    • rellig

      Public
      Python
      •
      Apache License 2.0
      •0•7•1•0•Updated Oct 31, 2024Oct 31, 2024

    • protvista-pdb

      Public
      PDB ProtVista Viewer
      JavaScript
      •
      Apache License 2.0
      •8•10•0•1•Updated Sep 19, 2024Sep 19, 2024

    • arpeggio

      Public
      Calculation of interatomic interactions in molecular structures
      Python
      •
      GNU General Public License v3.0
      •20•96•10•6•Updated Sep 3, 2024Sep 3, 2024

    • ner_for_protein_structures

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Aug 5, 2024Aug 5, 2024

    • afdb-notebooks

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•1•0•0•Updated Jun 5, 2024Jun 5, 2024

    • pdbe-api-specifications

      Public
      Apache License 2.0
      •3•0•0•1•Updated Dec 7, 2023Dec 7, 2023

    • pdbecif

      Public
      A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB"
      Python
      •
      Apache License 2.0
      •4•37•3•0•Updated Oct 30, 2023Oct 30, 2023

    • pdb-topology-viewer

      Public
      PDB Topology Viewer
      TypeScript
      •
      Apache License 2.0
      •4•5•1•16•Updated Oct 10, 2023Oct 10, 2023

    • pdb-sequence-viewer

      Public
      PDB Sequence-feature Viewer
      JavaScript
      •
      Apache License 2.0
      •1•3•0•0•Updated Apr 17, 2023Apr 17, 2023

    • pdb-rna-viewer

      Public
      The PDB RNA viewer depicts the secondary structure of a RNA in a 2D representation
      TypeScript
      •
      Other
      •3•3•2•1•Updated Mar 3, 2023Mar 3, 2023

    • pdb-redo

      Public
      PDB_REDO
      JavaScript
      •2•0•2•19•Updated Jan 6, 2023Jan 6, 2023

    • pdb-prints

      Public
      TypeScript
      •0•0•0•15•Updated Jan 5, 2023Jan 5, 2023

    • ligand-env

      Public
      Public repository of the PDBe ligand environment component
      TypeScript
      •
      Apache License 2.0
      •0•1•1•0•Updated Feb 9, 2022Feb 9, 2022

    • AFDB-Dictionary

      Public
      AlphaFold Protein Structure Database Dictionary
      0•2•1•0•Updated Dec 7, 2021Dec 7, 2021

    • pdbe-aggregated-api-example

      Public
      A Jupyter Notebook with an example use case for the PDBe Aggregated API
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated May 13, 2021May 13, 2021

    • exp-pages

      Public archive
      Angular2 and Polymer components to display experimental information for a PDB entry
      TypeScript
      •
      Other
      •0•0•0•0•Updated Mar 12, 2021Mar 12, 2021

    • pdb-raw-exp-data

      Public
      Polymer component displaying related raw experimental data when available
      HTML
      •
      Other
      •0•0•0•0•Updated Jan 25, 2021Jan 25, 2021

    • api-webinars

      Public
      Study materials for the PDBe API webinar series in September 2020.
      pythonbioinformaticstutorialpdbweb-componentsprotein-structureproteinapi-restwebinarjupyter-notebooks
      Jupyter Notebook
      •2•5•0•0•Updated Oct 22, 2020Oct 22, 2020
    0