PDBe API webinar series
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
PDBe API webinar series
»
Index
Index