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LBM-EPFL / PeSTo

Geometric deep learning method to predict protein binding interfaces from a protein structure.
https://pesto.epfl.ch
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Question: which prediction file(s) to use #11

Open yzhang-github-pub opened 1 year ago

yzhang-github-pub commented 1 year ago

Dear Authors,

Thanks for developing this very useful tool. I did a test on a PDB structure. The tool generated 5 files (with names of *_i[0-4].pdb). The b factor column in each of the five files is different. I didn't find documents about the these files. Please advise on how to use the files for interface inference, such as meaning of b factor column in each file, and cutoffs (like the mean values in a window and size of window to call interface, etc. Thanks!

ParthBibekar commented 11 months ago

The [0-4].pdb files are for predictions on protein-protein, protein-nucleic acid, protein-ion, protein-ligand, and protein-lipid, respectively. You can visualize the outputs in pymol using spectrum b, blue_white_red, all, 0, 1 or in ChimeraX using color bfactor palette "#2B59C3:#D1D1D1:#D7263D" range 0,1

Also consider using the web-server: pesto.epfl.ch/