Protein Close Residues Lifting (Graph to Hypergraph)

[bertranMiquel]

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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[levtelyatnikov]

Please consider making the tests pass to make this submission valid for the challenge

[levtelyatnikov]

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 [email protected] 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)
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• the output domain of the method you implemented
• your pull request number (Protein Close Residues Lifting (Graph to Hypergraph) #37)

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: Protein Close Residues Lifting - Input domain: Graph - Output domain: Hypergraph - Pull request: #37 <#37> Best, Bertran Missatge de levtelyatnikov ***@***.***> del dia dl., 8 de jul. 2024 a les 18:47:

…

Hello, @bertranMiquel <https://github.com/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 ***@***.*** 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 (#37 <#37> ) 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. — Reply to this email directly, view it on GitHub <#37 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHTIUTXCHDUYK7DS3SMXI2LZLK7DDAVCNFSM6AAAAABKRAMABSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUGY3TMNRUGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>