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HannesStark / EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
MIT License
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Measure of inference quality #24

Closed hmms117 closed 2 years ago

hmms117 commented 2 years ago

Hi,

First of all, thanks for developing this method - it is really something new.

When using the inference_from_files mode to infer various ligand conformations on several protein targets, how does the tool report some measure of inference quality"? Do you have some measure of conformation fit to the target? I can see intersection_losses_untuned being reported - can it be used?

Many thanks!

HannesStark commented 2 years ago

Hi!

EquiBind does (currently) not provide a confidence score or something similar to a docking score which could be used for ranking. If the intersection loss is unusually high it would indicate that there are intersections with the receptor and the conformation is likely not the best. However, this could also be seen in a visual inspection.

hmms117 commented 2 years ago

Thanks for the swift response! Ok, so for testing EquiBind for ranking, following EquiBind, we could try to run the (slower) tools to obtain a docking score.

With visual inspection, we see consistent clashes in our own test examples (PDB and ligands clashes). At inference time, are the PDB coordinates also adjusted? This happens in some docking tools. Do we need to save the PDB coordinates along with the ligand coordinates in inference_from_files? We are testing on single chain PDB files and a ligand in .sdf format.

Again, thanks for developing the method!

HannesStark commented 2 years ago

for testing EquiBind for ranking, following EquiBind, we could try to run the (slower) tools to obtain a docking score.: correct!

The coordinates of the receptor are not adjusted if that is what you are asking. The receptor is treated as a rigid body.

The receptor files also need to be provided next to the ligand files. It does not matter whether they are provided as .pdb or .sdf. I am not sure whether that answers the question. Please let me know if unclarity remains!

hmms117 commented 2 years ago

Thanks! It makes good sense - we will try it out! :)