Surface Biochemical Features

[zqsaudience]

Dear Author， I hope this message finds you well.

I am currently working on a project involving protein structure analysis and I would like to inquire about obtaining Surface Biochemical Features of proteins. Specifically, I am interested in calculating properties such as hydrophobicity and electrostatic potential. could you tell me how can I obtain Surface Biochemical Features of proteins? Is there any available code to achieve this?

Best regards.

[JocelynSong]

Hi, basically we provide the biochemical features of the nearest atom to the vertex in the point cloud, of which the code you can find at preprocess/prepare_surface.py! For the specific values of each biochemical feature, the model will have them when checking a lookup table when we input the nearest atoms to the model, of which the code you'll find at fairseq/models/surface_protein_model.py