- May 17, 2022 at 12:38 pm #99509Wout_Van_EyndeGuest
Is it possible to run AutoGrow4 without docking, e.g. when the target isn’t known or hasn’t a validated structure? If yes, how would one do this and would you recommend this? I guess it is done by adjusting the .json file to that extent, but I am not too sure.
I have no experience in AI nor in programming, just a great interest in this field, so excuse me for the lack of knowledge.
Wout Van Eynde, student at KU Leuven
- July 29, 2023 at 6:55 pm #158773Jacob DurrantKeymaster
Thanks for reaching out and for your interest in AutoGrow4! The current version of the software uses a docking step to select the best molecules, but it should be possible to modify the source code to skip this step. Docking does plays a crucial role in the compound-selection process used to form subsequent generations, though, so I don't recommend skipping that step. Hope this answer helps!
- August 8, 2023 at 2:35 am #141455Dr. AmolGuest
On the same lines to the question above I take this opportunity to ask a somewhat similar question. I would like to use my own AIML based predictor instead of any of the docking programs. The AutoGrow4 research article mentions that "With the appropriate plugin code, virtually any method for docking and/or reassessing ligand binding can be integrated into AutoGrow4, including quantitative structure–activity relationship (QSAR) approaches,
ligand-similarity evaluations, etc.", however, there is not much information on how to do it. Any guidance in this direction is requested. Thanks in advance.
- August 8, 2023 at 2:38 am #158801Jacob DurrantKeymaster
Thanks for your interest, too, Dr. Amol. Replacing the docking programs with another metric shouldn't be too hard. Here's the class used for Vina docking, for example: https://github.com/durrantlab/autogrow4/blob/master/autogrow/docking/docking_class/docking_class_children/vina_docking.py
You might use that as a starting template to build a related class for your AIML predictor. Hope this helps!
- The topic ‘AutoGrow4 without docking’ is closed to new replies.