Fold and Dock – chains not in contact

[Anonymous]

Hi

I wonder if anyone can suggest a solution, I am attempting to perform a fold and dock calculation. however, in about 80% of the structures generated by Fold and Dock the chains are not in contact with one another. On top of this, in about 5% of the cases I have actual overlapping of the structures (eg a helix (Ca not just side chains) will exist in the same position for each monomer)).

The command I am using can be found here

Thanks for your help

Chris

[Anonymous]

You seem to be exploring things the developers haven’t tried yet. Here is what Ingemar (the symmetry author) has to say:

“
this is hard for me to respond to because I don’t know if the membrane scoring function is compatible with symmetry (he is using -abinitio:membrane etc). If not, then all sorts of weird artifacts can happen. I know someone in the Bakerlab has used fnd to fold membrane proteins but I don’t know if they used the membrane scoring function. This was Ray Wang in the Baker lab, Yifan might now, and if not Vladimir perhaps?

If the membrane scoring is working with symmetry then I could look at it again.”

I’ve forwarded it along to those he suggested.

[Anonymous]

(Ray replied in the other thread: http://www.rosettacommons.org/content/can-fold-and-dock-protocol-applied-membrane-proteins#comment-4643 )

[Author]

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