[Jacob Durrant]

Hi Ziziphus,

Thanks for reaching out about the issue you encountered while using Webina. I appreciate your interest in the tool.

It's difficult to diagnose the error without access to the specific files you're working with. But, I suspect the problem arises when the protein becomes too large for the browser to handle because of the addition of hydrogen atoms (which are likely critical for accurate docking).

One potential workaround could be to select only the amino acids within a certain distance, such as 15 angstroms, of the binding pocket and dock into this smaller version of the protein. This solution isn't exactly elegant, but I suspect it would bypass the error.

I hope this helps!

Take care,
Jacob

[Jacob Durrant]

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!

~Jacob

[Jacob Durrant]

Hi Cassidy,

Thanks for reaching out about the DNA docking issue you're experiencing. It's challenging to troubleshoot the error without having access to the specific files. For what it's worth, I recently tested a protein-DNA complex from the PDB using Webina, and it successfully docked without encountering any "no such file or directory" error. It's possible that there may be an issue with the formatting of your files. But, without further information, providing a more precise solution is difficult.

Sorry for not being able to offer more concrete help!

~Jacob

[Jacob Durrant]

Hi Nilesh. Thanks for reaching out about the installation of Autogrow4. I appreciate your interest in our software. It seems that the issue you encountered is related to RDKit, which my group does not maintain. I recommend contacting the RDKit developers directly. They would be better equipped to help you in this case. Best of luck with your project.

[Jacob Durrant]

Hi David. Thanks for reaching out re. your FPocketWeb results. Nothing in our implementation of fpocket (FPocketWeb) introduces a random element, so I would guess that fpocket itself, the program on which our project is based, is non-deterministic.

To get a more definitive answer, I recommend contacting the developers of the original fpocket program. They would have a deeper understanding of the code base and could provide insights into any non-deterministic factors that may influence the scoring differences you saw.

I hope this information helps! Thanks again for your interest in FPocketWeb.

[Jacob Durrant]

Hi Lin,

Thanks for reaching out and expressing your interest in Gypsum-DL. I appreciate your feedback. It's a known limitation of the program, unfortunately. Our initial focus in creating Gypsum-DL was to prepare ligands for docking, so changing ligand coordinates didn't matter so much. But your use case is also perfectly reasonable.

I recommend using a program like Open Babel, which allows you to protonate ligands at a specific pH. I believe Open Babel's -H flag does a pretty good job, and it doesn't change the atomic coordinates.

I hope this suggestion helps! All the best.

[Jacob Durrant]

Much thanks for your interest in BINANA. Please do feel free to integrate it into your website. It has an open-source license precisely to encourage broad adoption. If you wouldn't mind, please let me know what website you end up integrating it into! It's great to know how the program is being used. Thanks again.

[Jacob Durrant]

Thanks for your interest in AutoGrow4. If your goal is to combine two ligand molecules and perform docking, I recommend editing the two molecules directly in a program like Avogadro and performing the docking separately. Autogrow is not specifically designed for this task. Best of luck with your project!

[Jacob Durrant]

Thanks for reaching out about the issue you're experiencing with POVME. Based on the error message you provided, it seems POVME is encountering a memory allocation error due to the combination of small grid spacings and large radii. I recommend increasing the grid spacing to ensure POVME does not exceed the available memory on your machine. Best of luck with your project.

[Jacob Durrant]

Much thanks for your interest in AutoGrow4. It's difficult to debug without more details, but I would guess that one or more of your starting compounds includes an atom that is not present in the Vina force field. It could be something like a boron atom, which I think can cause problems. I recommend checking the Vina documentation for more information. Take care.

[Jacob Durrant]

Thanks for reaching out and for your interest in Autogrow. It seems like your question is more related to the Vina scoring function, which is maintained by a different group. For any specific inquiries about Vina, I recommend contacting that group directly.

That said, Autogrow is not currently configured to work with custom versions of Vina. It might be possible to modify the source code to accommodate your needs. Alternatively, if you are looking for a docking program that allows for custom scoring functions, you might consider exploring Smina. Smina is based on Vina but offers the flexibility to incorporate custom scoring functions.

I hope this information helps! Thanks again for your interest.

[Jacob Durrant]

Thanks for reaching out re. BINANA. If you include the cofactor as part of the receptor along with the protein, BINANA should be able to detect interactions between the ligand and cofactors. You can capture the relevant interactions by considering the cofactor as part of the receptor. I hope this answer helps!

[Jacob Durrant]

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!

[Jacob Durrant]

Hi Thibault,

Thanks for reaching out about LigGrep! I appreciate your interest in the software. Currently, LigGrep cannot filter based on the Vina energy score. It focuses on atomic interactions.

All the best,
Jacob

[Jacob Durrant]

Hi Mike. When you say the computer hangs completely, do you mean your browser hangs, or the entire computer (requiring a reboot)? If it’s your entire computer, it might be a problem with your video card. Are you using a fairly outdated computer, by chance?

If it’s the browser, I wonder if you have the same problem when you use our server: https://durrantlab.pitt.edu/deepfrag/ ? If not, then it’s likely a problem with your server settings. You could use Google Chrome’s Developer Tools to look for errors that might help with debugging.

Hope this helps.

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