These interactive Python notebooks will guide you through various ways of programmatically accessing Protein Data Bank in Europe (PDBe) and Knowledge Bank (PDBe-KB) data using REST API
The REST API is a programmatic way to obtain information from the PDB and EMDB. You can access details about:
sample
experiment
models
compounds
cross-references
publications
quality
assemblies and more…
For more information, visit https://www.ebi.ac.uk/pdbe/pdbe-rest-api.
Recently we introduced a novel REST API that takes advantage of graph database Neo4J. This API contains a lot more value added annotations from PDBe and partner resources and is available from: https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/
Either use Binder to use the notebooks:
Or
You will need to have Jupyter installed on your machine. For Linux/OSX machines, simply type:
pip3 install --upgrade pip
pip3 install jupyter
For Windows machines (optionally also for Linux/OSX) you can install Jupyter with Anaconda: https://www.anaconda.com/download/
If installing using Anaconda, there is no additional prerequisites. If installing using pip3, you will need to have Python3 on your machine, and of course pip3
From command line on Unix machine these would be the steps setting up everyone:
mkdir pdbe_jupyter
cd pdbe_jupyter
git clone https://github.com/PDBeurope/pdbe-api-training .
jupyter notebook
Jupyter Notebook will open a window in your browser, and you can select the specific notebooks you would like to view.
Thanks to the PDBe team for suggestions during creating these materials