What are the Nodes and Edges of GraphMHC?

[ddiem-ri-4D]

Hi @recognizability Can you tell me what each Node and each Edge of a peptide and MHC is, and what these numbers mean?

Thank you very much. Mỹ Diễm.

[recognizability]

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0291223 In the paper, I specified in Fig 1 that the number of node features is 31 and the number of edge features is 12. Meanwhile, looking at Supplementary Table S2, I mentioned that the median number of nodes is 737 and the median number of edges is 1502. In other words, in the heat maps for the nodes and edges in the middle of Fig. 1, the x-axis corresponds to the feature and the y-axis corresponds to the number.

[ddiem-ri-4D]

Hi @recognizability I am wondering, in the context of Atomic features, are they the features of Peptide and MHC? So what does each Node represent? Is it the SMILES of the molecular formula? That means for each Peptide+MHC pair, you will have 31 Atomic features. What does each node represent? I am not yet asking about the encoding of the information. Is each Node a SMILES of the Peptide and MHC?

[recognizability]

As you can be seen from the pipeline in Fig 1 and the section "Conversion from the molecular structure of amino acids to dataset of interatomic graph structures", the MHC and peptide sequences are converted into graph structures through SMILES representation and the RDKit library. If you look at S2 Fig, you can see a graph of atomic nodes and the connections between them.