- This topic has 2 replies, 2 voices, and was last updated 1 day, 20 hours ago by NE.
- September 16, 2021 at 1:41 am #45911Cory KornowiczGuest
Recently, AutoDock Vina received an upgrade to version 1.2.2 with native python bindings. What are your/community thoughts on upgrading the implementation in AutoGrow 4? Looking through the bindings, it appears that it could almost completely make the use for docking classes obsolete, or at the minimum, relieve the need for hardcoded executable names. It also offers the possibility of reducing the parameters of hardcoded execution, and I noted that the ligand box could be autogenerated. There is also the potential of using the generated maps for informed fragment choice decisions (potential new feature?).
I am a current student researcher in Bioinformatics and have been pondering some form of pharmacological-informed fragment addition; however, while I currently do not attend Pitt, I would be more than happy to contribute anything I can!
- September 16, 2021 at 1:44 am #45978ikk6Keymaster
Hello, Cory. Thank you for the information, that’s interesting. I will notify the lab. That said, I don’t think the project has an active maintainer since the previous person graduated. That’s the opportunity!
- December 15, 2021 at 1:46 am #60418Jacob DurrantKeymaster
Hi Cory! I recently saw the Vina 1.2 update, which seems to have a lot of great additions. I agree with you that the multiple-ligand docking feature could be great for fragment growing!
One of the advantages of having AutoGrow use an executable rather than python bindings is broad compatibility. Most docking programs don’t have Python bindings, but all have executable files.
Given your interest in fragment-growing strategies, have you had a chance to look at our lab’s DeepFrag program? https://durrantlab.pitt.edu/deepfrag/ We’re very excited about machine-learning approaches to drug discovery.
Anyway, I just wanted to thank you for your interest! It’s always great to engage with people who like to think about these kinds of things.