Dear all,
I am working with five proteins and would like to investigate their interactions when present together in a single solution. Could you suggest any online tools or platforms capable of performing molecular docking for multiple proteins simultaneously?
Thank you for your assistance.
Best regards,
AlphaFold 3 - https://alphafoldserver.com/
GROMACS MD in Google Cloud - https://github.com/paulshamrat/ColabMDA
OpenMM in Google Cloud - https://github.com/pablo-arantes/making-it-rain
Hi,
You can try HADDOCK which is a great platform for multi-protein docking. It is powered by molecular mechanics and even allows coarse-graining for larger complexes.
https://rascar.science.uu.nl/haddock2.4/
To refine your docking setup, PeSTo (Protein Structure Transformer) is useful for predicting protein binding sites on your proteins which can then be defined as active residues for docking with HADDOCK.
https://pesto.epfl.ch/
If you're exploring beyond traditional docking, AI-based tools like AlphaFold are worth considering for predicting multi-subunit protein assemblies even though they are not docking tools.
https://alphafoldserver.com/about
Hope this helps!
Yes, use ClusPro, HADDOCK, or PatchDock for multi-protein docking. For large complexes, RosettaDock is effective.
All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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