search

biomed-AI / DiffDec

MIT License
28 stars 5 forks source link

how to use a specific protein pocket and for a specific molecule #3

Closed MachineGUN001 closed 9 months ago

MachineGUN001 commented 9 months ago

hi,

Thanks a lot for offering such an interesting program, very good work. Acknowledgement. Here is the question, I would like to ask how to make R group changes for a specific protein pocket and for a specific molecule as you have shown in your article, such as PDB , 4iiy and 4ja8. if I want to change to another protein structure as well as to a new compound, how should I use the run script? coud you please provide an example or tutorial for the process? or could you pleaes provide the example data with scaffolds/Rgroups/protein pdb file etc for format exaplanation? in the line of process_and_prepare.py，single_train.smi，what format is it?

Thank you very much!

Best,

S-y

XJJBot commented 9 months ago

Hi, thanks for your interest in the work. We have uploaded relevant code for sampling with a specific protein and scaffold and provided some examples. Additionally, regarding the single_train.smi in process_and_prepare.py, it is created by Lib-INVENT-dataset repo (https://github.com/MolecularAI/Lib-INVENT-dataset). We also provide corresponding examples for it.

MachineGUN001 commented 9 months ago

hi, @XJJBot thanks for your kind explanation.

I also noted that the smi file as the output SMILES file in lib-INVENT repo that will contain three columns including scaffolds, decorations and the original compounds. however, the lib-INVENT needs to be implemented in linux, and I have some trouble in runing that.

thus, could you please provide some expamles for single_train.smi generated by Lib-INVENT-dataset repo? it'd be great to try your codes mainly for testing if that works on the specific proteins with specific new molecules.

many many thanks,

Best, Sh-Y

XJJBot commented 9 months ago

You may try the newly uploaded codes sample_single_for_specific_context.py and sample_multi_for_specific_context.py, and the relevant instructions are updated in README accordingly.

MachineGUN001 commented 9 months ago

You may try the newly uploaded codes sample_single_for_specific_context.py and sample_multi_for_specific_context.py, and the relevant instructions are updated in README accordingly.

that works well,

Thank you very much for your help, your code is very high quality and clear!!

many thanks,

ShY