Notebooks¶
Jupyter notebooks show how to use protein-quest through its Python API and can be run in cloud notebook environments or locally.
Available notebooks¶
| Notebook | What you will do |
|---|---|
| Search UniProt | Find UniProt accessions and map them to PDB, AlphaFold, EMDB, and partner datasets. |
| AlphaFold | Download AlphaFold models, filter on confidence, and visualize structures with Mol*. |
| PDBe | Download PDBe structures, extract single chains, and visualize structures with Mol*. |
Launch in cloud environments¶
| Notebook | Google Colab | notebooks.egi.eu | Binder | nbgitpuller |
|---|---|---|---|---|
| Search UniProt | Open | Open | Open | Generate link |
| AlphaFold | Open | Open | Open | Generate link |
| PDBe | Open | Open | Open | Generate link |
- notebooks.egi.eu requires sign-in and VO enrollment before use.
Run notebooks locally¶
- Install Jupyter.
python -m pip install jupyterlab
- Install notebook dependencies.
python -m pip install protein-quest[nb]
(The [nb] extra installs molviewspec for structure visualization in the
AlphaFold and PDBe notebooks.)
- Start Jupyter and open a notebook.
jupyter lab