The protein of my interest is forming isopeptide bond with another protein. Is it possible to do this with any free software?
Thank you for your response.
In Rosetta online server, there is no option to mention that the residues must be interacted by covalent bond. Is it possible with offline version.
I found that HADDOCK Guru interface facilitates this. But unfortunately i do not have access. So, is there any other way?
Dear Manish,
Unfortunately there is no accurate tool or software for the protein- protein covalent incarceration or docking. You have the options for covalent docking in HADDOCK and ClusPro. But the prediction is not always accurate and you can get more information in these two papers and they have further information on the covalent docking of proteins.
You can use these tools but before setting constrains for the covalent docking, your input structures must be accurate and make sure your constrains have enough literature data support.
All the best
http://onlinelibrary.wiley.com/doi/10.1002/prot.24403/full
http://onlinelibrary.wiley.com/doi/10.1002/prot.24428/full
ZDOCK, RDOCK, DOT, HEX, RosettaDock, as well as GRAMMX Server may be used for protein-protein docking.
Dear Manish Kesherwani,
It is not problem you do not have a GURU interface account. Because if you e-mail Bonvin (leader of HADDOCK) kindly, he will help you about the account. Furthermore, you can try additional but harsh techniques. I do not know how efficient this is but you can carry out QM/MM simulations.
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