PointCloud to Graph Protein Lifting (PointCloud to Graph)

[bertranMiquel]

This notebook shows how to import UniProt protein data and convert it to a graph using the PointCloudToGraph class. Proteins are represented as point clouds where each point is a residue in the protein, setting CarbonAlpha as its centers. The graph is created by connecting residues that are close to each other in the 3D space or that appear in a sequential order.

The point cloud 3D domain is lifted to a graph defining the edges between its nodes in the following way:
- 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.
- KNN: Connecting residues that are close to each other in the 3D space. This approach is based on the physical proximity of the residues in the protein structure.

Additionally, we have also included the following features to the graph:

• Node key: One-hot encoding per each residue type.
• Pos: position of the residues in the 3D space.
• Edge features: angle (direction between CarbonAlpha (CA) and CarbonBeta (CB) atoms of each residue between different residues) and distances between the connected residues.

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[gbg141]

Hello @bertranMiquel! Thank you for your submission. As we near the end of the challenge, I am collecting participant info for the purpose of selecting and announcing winners. Please email me (or have one member of your team email me) at guillermo_bernardez@ucsb.edu so I can share access to the voting form. In your email, please include:

• your first and last name (as well as any other team members)
• the title of the method you implemented
• the input domain of the method you implemented
• the output domain of the method you implemented
• your pull request number (PointCloud to Graph Protein Lifting (PointCloud to Graph) #42)

Before July 12, make sure that your submission respects all Submission Requirements laid out on the challenge page. Any submission that fails to meet this criteria will be automatically disqualified.

[bertranMiquel]

Hi Guillermo, Answering to fulfill the submission requirements: - Name and last name of the participants: Bertran Miquel-Oliver, Manel Gil-Sorribes, Alexis Molina, Victor Guallar (all of them in cc) - Title: PointCloud to Graph Protein Lifting - Input domain: PointCloud - Output domain: Graph - Pull request: #42 <#42> Best, Bertran

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