Ligand Docking Simulation Programs

Question

[ac.research]

I have am looking to run ligand/receptor docking simulations to identify how a ligand binds to its receptor.

What are the best software to use?

[ac.research]

No not molecular dynamics (Gromacs), a program similar to AutoDock (which seems its autodocktools no longer installable in new operating systems since 2014) hence why I am asking for other programs.

[prasundutta87]

You can use autodock Vina...its very fast and is available in binary version..

[ac.research]

yes, but AutoDockTools no longer works in new operating systems since 2014, it has not been updated since 2014 and thus is not compatible with new Python libraries (or something like that) -> it gives this error (ImportError: numpy.core.multiarray failed to import). In summary AutoDockTools does not work anymore.

[prasundutta87]

autodock Vina is different from autodocktools and not part of it so you may not face this particular python issue there..check this website: http://vina.scripps.edu/ and its FAQ part about the differences..it has its own binaries..

You are right that its a Python version issue and I faced it long back and I solved it by installing an older version of python, don't remember which one though as it was in my old lab server..

[ac.research]

I tried that (forum link of my question: https://www.biostars.org/p/266917/#266953).

And you are right, AutoDock Vina (works nicely) is different from AutoDockTools (does no work). Unfortunately you cannot run AutoDock Vina without preparing and converting the .pdb files to .pdbqt files using AutoDockTools.

If there is a way to use AutoDock Vina without AutoDockTools that could solve my problem. But since I cannot find a way through my internet searches I am looking for a different program altogether.

[prasundutta87]

I can suggest one thing..check out this Galaxy instance: http://mpds.osdd.net/

Go to data analysis-->Docking and follow the instructions..

All the required steps are performed internally and you don't require to install any tools or binaries or think about software versions anymore..Vina is implemented as a docking tool in Galaxy..A manual is also present to guide new users..

If you face any issues, required email addresses are mentioned in the 'Contact' page as well..

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Answer 1

[prasundutta87]

Are you referring to molecular dynamics simulations that is performed after docking experiment?