Constructing Graphs from AlphaFold Protein Structure Database

In this quick tutorial we show how to construct graphs from the AlphaFold Protein Structure Database. This is a fantastic resource for the community and we hope to make it more accessible to the Geometric Deep Learning community!

It’s plug and play with the top-level `graphein.protein.construct_graph() <https://graphein.ai/modules/graphein.protein.html#graphein.protein.graphs.construct_graph>`__ function; however we now require UniProt identifiers.

We also provide a utility `graphein.protein.utils.download_alphafold_structure() <https://graphein.ai/modules/graphein.protein.html#graphein.protein.utils.download_alphafold_structure>`__ to download PDBs and associated metadata (aligned error scores as an accompanying JSON file). There is also an equivalent function for downloading structures from RCSB. After downloading the structure, simply use Graphein to compute the graph as you normally would. You can check out the `residue_graphs.ipynb <https://graphein.ai/notebooks/residue_graphs.html>`__. notebook tutorial to go deeper into protein graph construction utilities in Graphein.

Quickstart

The structures are accessed via their UniProt accession codes.

Here, we’ll be looking at `Q8W3K0 <https://alphafold.ebi.ac.uk/entry/Q8W3K0>`__, a rather beautiful model of a protein with a not-so-catchy name: Probable disease resistance protein At1g58602.

# Install graphein if necessary
#!pip install graphein

import graphein.protein as gp

g = gp.construct_graph(uniprot_id="Q8W3K0")
gp.plotly_protein_structure_graph(g, colour_nodes_by="plddt") # Colouring by plDDT shows the assigned confidences!

Reading PDB file...         ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
Processing PDB dataframe... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
Initializing graph...       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0% -:--:--

Data type cannot be displayed: application/vnd.plotly.v1+json

Downloading Structures

First, we need to download the strutures from AlphaFoldDB. One can download either the structure alone or together the aligned scores as a JSON.

from graphein.protein.utils import download_alphafold_structure

# Download the PDB file for an example protein (UniProt: Q8W3K0) with the aligned score
protein_path = download_alphafold_structure("Q8W3K0", out_dir = "/tmp", aligned_score=True)
protein_path

('/tmp/Q8W3K0.pdb', '/tmp/Q8W3K0.json')

# Download the PDB file for an example protein (UniProt: Q8W3K0) without the aligned score
protein_path = download_alphafold_structure("Q8W3K0", out_dir="/tmp", aligned_score=False)
protein_path

'/tmp/Q8W3K0.pdb'

Constructing the Graph

We show a simplified workflow here. For more information and a fuller exposition of the features, please refer to the Residue Graph Tutorial.

First, we require a config object.

# Load the default config
c = gp.ProteinGraphConfig(granularity='CA')

# Construct the graph!
g = gp.construct_graph(path=protein_path)

# Plot
gp.plotly_protein_structure_graph(g, node_size_multiplier=0.5, colour_nodes_by="residue_name")

Reading PDB file...         ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
Processing PDB dataframe... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
Initializing graph...       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0% -:--:--

Data type cannot be displayed: application/vnd.plotly.v1+json

Adding Edges

What if we want to add some more edges to the graph? Well..

Documentation for edge funcs

config = gp.ProteinGraphConfig(edge_construction_functions=[
                                gp.add_aromatic_interactions,
                                gp.add_cation_pi_interactions,
                                gp.add_hydrophobic_interactions,
                                gp.add_ionic_interactions
                                ]
)

g = gp.construct_graph(path=protein_path, config=config)

gp.plotly_protein_structure_graph(g, colour_edges_by="kind", colour_nodes_by="residue_name", label_node_ids=False, node_size_multiplier=2, node_size_min=5)

Reading PDB file...         ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
Processing PDB dataframe... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
Initializing graph...       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
Constructing edges...       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0% -:--:--

Data type cannot be displayed: application/vnd.plotly.v1+json

You can also check out our Residue Graph Tutorial for more customisation options!! For more details on visualisation, please refer to the interactive visualisation tutorial or the documentation.