I have to perform protein-protein docking in order to obtain a dimer from two protomer structures.
Even if I can infer the interacting surfaces from homolog dimers, I have no clues about contact restraints (ie applying NMR evidence to HADDOCK jobs).
Do you know any reliable protein-protein docking software (and possibly free) to accomplish such task?
Hi,
In principle you can use PIPER (Cluspro 2.0), HEX and Molsoft, but personally I can't trust to any of these "black box" solutions. You can also examine, by tools like Molsoft ODA, for potential differences between all available homolog dimers.
What I would make is to use the information from your homolog dimers and to obtain some initial complex that to be refined. You can use HADDOCK. Then use Molecular dynamics to refine your complex. Under MD I also mean some more advanced methods like accelerated MD (aMD). As an output you will obtain some number of clusters and you have to choice "the best one" based on their free energies and populations. Then you can refine further you complex by some regular MD. Indeed here I don't speak for a single 10ns run, but at least 4-6 independent 70-100ns simulations.
In fact I would not consider seriously any protein-protein docking and "final" complex (even with NMR evidence and HADDOCK) without above suggested or similar scheme.
Thank you Filp for the answer. I am really interested in accelerated dynamics. Could you suggest me any reference for this topic? (In particular accelerated dynamics with GROMACS)
Dear Dario
I send my best wishes to you.
For Pro-Pro docking, you can use of the following tools:
1- ClusPro web server (https://cluspro.bu.edu/login.php).
2- GRAMM-X (http://vakser.compbio.ku.edu/resources/gramm/grammx/)
3- PIPER (https://www.schrodinger.com/piper)
4- PyDock (https://life.bsc.es/pid/pydock/)
5- KBDOCK (http://kbdock.loria.fr/)
Notice, among above tools I recommend you for use of ClusPro web server and pyDock. If you can access to Schrodinger package, it can help you better than the others. Among these tools ClusPro is easy and user friendly for running a molecular docking.
All the best!
Res. Ass. Hassan Rasouli
Medical Biology Research Center, Kermanshah University of Medical Science.
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