Protein Close Residues Lifting (Graph to Hypergraph)

The UniProt dataset is a custom dataset that is created by fetching data from the UniProt API. The dataset is created by fetching a list of proteins based on a query and then fetching the structure of each protein using the AlphaFold API. The dataset is then created by creating a graph for each protein where the nodes are the residues and edges are the connections between residues. These connections are usually done by the closeness of the residues. In this example, we connect the residues in two ways, representing the data into a graph:

• Sequentialwise: Connecting residues that appear in a sequential order (one after another). This approach is based on the presence of peptide bonds, which link the amino acids in a protein chain in a specific sequence.
• Closewise: Connecting residues that are close to each other (under than a threshold) and the direction between CarbonAlpha (CA) and CarbonBeta (CB) atoms of each residue are less than 90 degrees between different residues. This approach ensures that residues are connected when they are in close proximity and have a similar orientation, indicating that their spatial arrangement and orientation are biologically appropriate (the residues are appropriated with a similar orientation).

The target variable is the mass of the protein.

This representation can be improved by lifting it to an hypergraph. As done in Jiang et al. (2021), we will create an hypergraph by grouping the connected residues that are close to each other (less than a parameter).

This pull request is done under the team formed by: Bertran Miquel Oliver, Manel Gil Sorribes, Alexis Molina

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From https://github.com/pyt-team/challenge-icml-2024/pull/37