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LPDI-EPFL / masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
Apache License 2.0
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How can I get ground truth? #21

Open ElvisRain opened 3 years ago

ElvisRain commented 3 years ago

image I would like to get other proteins' ground_truth '.ply' files,where can I search it?

pablogainza commented 3 years ago

Sorry for the late reply!!

So if you want the ones used in the paper, you can download them from zenodo https://doi.org/10.5281/zenodo.2625420

If you want the ground truth for a specific protein, you can compute it the docker version, something like this:

cd masif/data/masif_site/
./data_prepare_one.sh 1BRS_A
cd data_preparation/01-benchmark_surfaces/

There you would find the file 1BRS_A.ply with the groundtruth

The groundtruth is computed by first generating the surface of the chain you selected (e.g. 1BRS_A) and then generating the surface of everything that comes in the pdb file. The ground truth is then defined as those points in the monomer that are farther than 2 angstroms from any point in the surface of the whole PDB file.