PDBe API webinar series Logo
1.0
  • Introduction to PDBe programmatic access
  • Searching with the PDBe API
    • PDB search
      • 1) Making imports and setting variables
      • 2) a function to get data from the search API
      • 3) formatting the search terms
      • 4) Getting useful data out of the search
      • 5) running a search
      • 6) Analysing and plotting the results
      • 7) searching for two terms at once
      • Questions to answer
    • PDB sequence search
      • 1) Making imports and setting variables
  • Creating complex PDBe API queries
  • Using the PDBe Graph API
    • Introduction
      • Using the documentation
    • Usecases
      • Predicted ligand binding sites in interaction interface
        • 1) Get the annotations data for UniProt accession P61626
        • 2) Filter the data for providers p2rank and 3dligandsite
        • 3) Get interacting residues for the UniProt accession
        • 4) Filter interface_data on common residues
      • Accessible residues for a PDB structure
        • 1) Get the 3Dcomplex annotations for PDB entry 3pxe
        • 2) Filter the data for ASA_alone label
        • 3) Filter site_residues on raw_score > 0
  • PDBe tools in GitHub
    • pdbecif
      • Structure reading
        • Dictionary output
        • CIFWrapper output
        • CifFile output
      • Structure writing
    • pdbeccdutils
      • Structure reading
      • Component object
        • Scaffolds
        • Fragments
        • Molecular depictions
      • Structure writing
      • Parity method
      • Scripts
    • arpeggio
      • Precomputed data
      • Example
      • arpeggio script
      • arpeggio API
      • Excercise
  • Data visualisation at PDBe
    • PDB Component Library
    • Example Links
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