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mattragoza / LiGAN

Deep generative models of 3D grids for structure-based drug discovery
GNU General Public License v2.0
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How to use PDB of Alphafold2 to drug discovery? #44

Closed lh12565 closed 2 years ago

lh12565 commented 2 years ago

Hi @mattragoza I want to use pdb of alphafold2 to find molecules. Do I only need to change two parameters: data_root and data_file in config/generate.config? Is the 'crossdock2020' the default reference files? for example:

data_root: data/ data_file: data/alphafold.pdb

Thanks!

mattragoza commented 2 years ago

Please refer to #40. I will update the readme with better instructions for this usage, as well.

lh12565 commented 2 years ago

Please refer to #40. I will update the readme with better instructions for this usage, as well.

Hi @mattragoza there is no ligand in pdb of alphafold. My parameter file (data_file) is as follows: 1 0 0 data/alphafold.pdb 0 #0 As I have no ligand and RMSD, Is that right? Thanks!

mattragoza commented 2 years ago

You still need to provide a ligand structure file to the model, even if you are only interested in prior sampling. You can use something like tests/input/O_0_0_0.sdf, which just contains a single oxygen atom. The ligand structure will not be used by the model if you perform prior sampling, but this is just the expected data file format for now.