Jacob Durrant

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Viewing 15 posts - 1 through 15 (of 90 total)
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  • in reply to: PVR vs Oculus Quest2 #94247
    Jacob Durrant
    Keymaster

    Hi Christian. Thanks for your interest in ProteinVR. I tested your protein on the Oculus browser. The frame rate wasn’t as high as I hoped, but it did work. I wonder if your device might be underpowered in terms of memory. What kind of Oculus headset do you have? Thanks.

    in reply to: Integrating the Vina 1.2.2 Update #60418
    Jacob Durrant
    Keymaster

    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.

    in reply to: Halogen bond interaction #47938
    Jacob Durrant
    Keymaster

    Hi Sarath. Much thanks for your interest in BINANA, and for pointing out the need for this new feature. I added an issue to the BINANA repo as a reminder for a future version. Not sure when the next version will be released (we actually just released a new one a few weeks ago), but that issue should keep it on my radar. Here are some BINANA-related links, in case you’re interested:

    Version 2.0 (just released): https://git.durrantlab.pitt.edu/jdurrant/binana
    Web app: https://durrantlab.pitt.edu/binana/

    Thanks!

    in reply to: Ligand docking pose view #44745
    Jacob Durrant
    Keymaster

    Hi Brandon. Much thanks for your interest in AutoGrow4. Without seeing your files, I can’t say for certain what the problem is. But for what it’s worth, I don’t think the SDF files contain the docked compounds. If I’m not mistaken, the docked poses end in ".pdbqt.vina" and are PDBQT formatted. I hope this helps. ~Jacob

    in reply to: Possibility to extend to DNA #40575
    Jacob Durrant
    Keymaster

    Hi Alok. Much thanks for your interest in AutoGrow4. To answer your question, there unfortunately isn’t a video describing AutoGrow4 use. But here’s some documentation that might help:

    https://git.durrantlab.pitt.edu/jdurrant/autogrow4/-/blob/4.0.3/README.md

    https://git.durrantlab.pitt.edu/jdurrant/autogrow4/-/blob/4.0.3/tutorial/TUTORIAL.md

    By default, I believe AutoGrow4 uses AutoDock Vina for docking under the hood. I don’t know how well Vina performs when using DNA as the receptor, but in principle it might work. At least some folks have tried it: http://www.chem.hope.edu/~discus/muccc/muccc30/MUCCC30-Haugen.pdf

    Hope this answer helps. Take care.

    in reply to: Deepfrag output seems to teleport ligand to (0,0,0) #40574
    Jacob Durrant
    Keymaster

    Hi Ben. Much thanks for your interest in DeepFrag! Just to clarify, DeepFrag doesn’t actually position the fragments it recommends in 3D space. It only suggests which fragments to add.

    As a helper program for the DeepFrag browser app, we created a separate app called Fuser that can be used to add the DeepFrag-recommended fragment to a source molecule. The output is a 3D model for use in docking studies. Are you referring to the Fuser app in your question, by chance?

    If so, it’s important to note that the 3D ligand made in Fuser isn’t meant to be in any sense "docked" into the protein receptor. DeepFrag doesn’t position the fragment (it only recommends what fragment to use), and Fuser is a step removed from DeepFrag.

    Hope this helps. Take care..

    in reply to: vina parameters #40573
    Jacob Durrant
    Keymaster

    Hi Luciano. Much thanks for your interest in AutoGrow4. Looks like you might need to use the ‘custom_docking_script’ parameter. Here’s a description:

    The name and path to a python script that is used to dock ligands. This is required for Custom docking choices. Must be a list of strings [name_custom_conversion_class, Path/to/name_custom_conversion_class.py]

    More information here: https://git.durrantlab.pitt.edu/jdurrant/autogrow4/-/blob/4.0.3/tutorial/TUTORIAL.md#running-custom-docking-scripts

    in reply to: ligand problem #38575
    Jacob Durrant
    Keymaster

    Hi Xiaoqing. Much thanks for your interest in AutoGrow4. It’s difficult to know what exactly is causing the problem based on the provided information, but let me give a few suggestions in case they help. The error might occur when none of the compounds of one generation pass the user-specified filters. You could try increasing the number of crossovers, mutants, etc., to give the program more chances to generate acceptable compounds for advancing to the next generation.

    It could also be that it’s not possible to add fragments to your starting compounds because your fragments (or starting compounds) lack the reactive groups that the AutoGrow4 reaction library requires.

    Another thing to try is to remove the -LipinskiLenientFilter parameter, which could allow more evolving compounds to advance to the next generation.

    Hope this helps,

    Jacob

    in reply to: Error file with multiple ligands #38571
    Jacob Durrant
    Keymaster

    Thank you, Sofea, for pointing out a useful new feature to include! Best of luck with your project.

    Jacob Durrant
    Keymaster

    Hi Christian. Thanks for all your interest in AutoGrow. Unfortunately, the ideal settings will depend very much on the initial population of ligands, both in terms of numbers and available chemical moieties where optimizing fragments can be added. I’d recommend trying a few different settings to see which one gives the best results. Take care.

    in reply to: ligand problem #37849
    Jacob Durrant
    Keymaster

    Hi Xiaoqing. Much thanks for your interest in AutoGrow. I suspect you’re getting this error because you are using AutoGrow settings that are too restrictive. AutoGrow appears to be unable to generate any compounds given those settings. It could also be that your initial starting compound(s) do not have any chemical moieties compatible with AutoGrow’s reaction library. This posting could also be helpful: https://durrantlab.pitt.edu/forums/topic/not-creating-ranked-ligand-file-during-lead-optimization-in-generation-0/

    Hope this answer helps. ~Jacob

    in reply to: Shifted coordinates in resulting .pdbqt and .pdb files #37847
    Jacob Durrant
    Keymaster

    Hi Patricio. Please forgive my delay in responding. I believe AutoGrow actually redocks the compounds with every generation by default. I suspect the file you’re seeing is the predocked ligand. I’d recommend redocking that compound back into the receptor using AutoDock Vina or some other program, independent of AutoGrow. I hope this answer helps. ~Jacob

    in reply to: Probability or ratio of each variant per ligand #37844
    Jacob Durrant
    Keymaster

    Hi Edward. Much thanks for your interest in Gypsum-DL. If I recall correctly, Gypsum prioritize the variants based on their predicted energies, according to RDKit. But there’s also a random component to the variant selection. If you’re not seeing some variants in the generated libraries that you think should be there, you might try allowing a larger number of variants per compound. I hope this helps. Take care.

    Jacob Durrant
    Keymaster

    Hi Jared. Much thanks for your question, and sorry for my delayed response. BlendMol is actually specifically designed not to change the coordinate frame. In my experience, many other ways of exporting molecular meshes do recenter the protein before export. I suspect whatever program you’re using to generate the ply file is the one that’s resetting the frame. Hope this answer helps. Take care.

    in reply to: Ball and Sticks model #37839
    Jacob Durrant
    Keymaster

    Hi George. BlendMol uses VMD to generate meshes "under the hood." You can also use VMD directly to set up your scene, and VMD does include a ball-and-sticks representation. You can then save the VMD scene as a visualization state file (. vmd extension) that you can load into Blender via BlendMol. Hope this answer helps.

Viewing 15 posts - 1 through 15 (of 90 total)