Is there any free online tool where I can do online docking studies of 1000 ligands with a single protein in a single step .

Question

[Manoj]

Is there any free online tool where I can do online docking studies of 1000 ligands with a single protein in a single step .

[Ram]

Please read Rule #7 in Ten Simple Rules - tell us what you've tried already.

Also, give us an idea of why you are trying to do what you're trying to do - it gives us a view of the bigger picture.

[keaun]

I might be biased, but I'd definitely recommend playing around with neurosnap to see if it makes sense for your use cases :).

The platform offers various tools for molecular docking including those for protein-protein, protein-nucleotide, and protein-ligand interactions. Additionally, you can further improve the quality of any screening process by using more ambiguous tools like AF2Bind or ScanNet that instead predict binding residues which can be used in conjunction with molecular docking approaches.

Molecular Dynamics is also available but is more advanced in terms of setting things up and interpreting results correctly.

Full disclosure, I am the founder of neurosnap, so if you have any questions or want further information, feel free to let me know!

Answer 1

[Sherry]

https://www.tamarind.bio/ worked great for me. They have a batch option that lets you run many thousands of ligands against the same receptor.

[Ram]

Are you affiliated with this company? If so, please declare your affiliation and create a Tool type post advertising your tool.

Also, is this also you: Sherry ?