NNScore Activity
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jdurrant
Activity for NNScore
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Douglas Houston posted a comment on discussion NNScore Help
Hi Jacob, I thought you might be interested in where this discussion went: https://pubmed.ncbi.nlm.nih.gov/35901959/ Best regards, Doug
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Hi Jacob, I was wondering if you had managed to dig up your old Python scripts for this? The call has gone out to advertise MSc projects and I'd like to offer one based on this, but I don't want to promise students anything until I have a starting point ... Best regards, Doug
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Hi Jacob, Many thanks for the very helpful reply! and 3. look straightforward, so I think the challenging bit will be 2. I don't have any experience with pyTorch or Tensorflow, but I was planning to learn one of them at some point anyway! If that proves too challenging I note that FFNET is still going, and has been updated to Python3 ... https://pypi.org/project/ffnet/ If you could provide your scripts and anything else that you think might be useful to get us started that would be really great....
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jdurrant posted a comment on discussion NNScore Help
Hi Douglas. Sorry for the delay. You're right that NNScore could use an update. It's remarkable how quickly the PDBbind database expands! :) I do think it would take a bit more to create a new version of NNScore than applying my existing scripts, though. Here are just a few things that come to mind: 1) It would need to be Python3 compatible, since Python2 will soon reach end of life. All my scripts are written in Python2. 2) It would probably be best if it used a more modern neural-network library...
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One thing that's occurred to me since re-reading the paper and watching your excellent talk on Youtube; NNScore was trained with PDBbind and MOAB, but it was a good few years ago and these databases have since grown greatly (DUD-E too). My guess is that NNscore's performance would get even better if it was re-trained, and that (definitely guessing this time!) it ought to be relatively straightforward since presumably all your tools and the data preparation and training pipeline shouldn't need changing...
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Ah yes, very helpful, thank you!
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Hi Dr. Houston. Much thanks for your interest in nnscore. I believe that error occurs when nnscore encounters two adjacent atoms with types that were not commonly found to be adjacent in the training data. Rather than trying to make a guess based on insufficient data, nnscore simply throws the error. In practice, though, the fact that these atoms are adjacent is probably a good indication that the pose is not correct. Hope this answer helps. All the best.
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Hi, OK I figured out how to create a new thread! I am running NNscore1 on my docking results, but I am seeing many pose evaluations fail with the following type of messages: The program can't deal with the PROXIMITY_4 calculation between ligand,receptor atom types: NA NA, ligand = t op1k932_largestC.pdbqt LIGAND: ATOM 21 N UNL d 1 13.118 -43.051 -2.497 -0.42 +0.02 -0.066 NA RECEPTOR: ATOM 463 ND1 HIS 145 16.675 -44.777 -2.032 0.00 0.00 -0.247 NA Average score: -999999.9 (bad binder) You can download...
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Hi jdurrant, I tried to make a new thread (you have to send an email??) but nothing appeared, so I'm posting here. I am running NNscore1 on my docking results, but I am seeing many pose evaluations fail with the following type of messages: The program can't deal with the PROXIMITY_4 calculation between ligand,receptor atom types: NA NA, ligand = t op1k932_largestC.pdbqt LIGAND: ATOM 21 N UNL d 1 13.118 -43.051 -2.497 -0.42 +0.02 -0.066 NA RECEPTOR: ATOM 463 ND1 HIS 145 16.675 -44.777 -2.032 0.00...
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Suhad Jihad posted a comment on discussion NNScore Help
Hi Dr Jocob, https://www.researchgate.net/publication/309457472_Testing_and_Development_of_Computer_Aided_Drug_Design_Tools_Including_Docking_and_Scoring...
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Hi Suhad. It seems both Vina and NNScore are giving you the same answer. Also, glycerol...
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Hi Dr Jacob, thank a lot for your response, no my files are 3D I attached them. The...
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Hi Suhad. If you're getting a vina score of zero, there might be something else wrong...
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Hi Dr Jacob, Thanks for help, I dock the programming cell death PD-1 and its ligand...
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Hi Suhad. Happy to help. As with other docking programs, NNScore isn't well suited...
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Hi Dr Jacob, Kindly I have this question : When I try using nnscore with my files...
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farynaa posted a comment on discussion NNScore Help
What's wrong with it? Traceback (most recent call last): File "NNscore2.py", line...
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Hi Suhad. Sorry for my delay. 1) They are right in recognizing that NNScore isn't...
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Hi Dr., Thanks a lot and sorry for this confusion. Ok I have these comments : 1....
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Hi Suhad. I'm happy that the ODDT authors have included an nnscore-like scoring function...
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Very happy you were able to get this to work, Suhad. Thanks again for your interest...
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Thanks alot Dr Jacob D. Durrant for your helpful Notes finally I get this result...
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Hi Suhad. I can't be sure without seeing your files, but I wonder if your ligand...
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Thanks alot for the update and the networks files .... Now the error may be clear...
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When I use NNScore command suhadjihad@Suhad:/home/suhadjihad$ python /home/suhadjihad/NNScore2.py...
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