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protein interface design

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protein interface design

Hello All

I want to design the interface of a two-chain complex( actually design only one of the partner)  using raf / rac design script which I have attached it here.

Is it better and more accurate to change this script in order to get and use resfile ? 

I prefer to design interface automatically without resfile (just script defines interface residues)  because I have no idea about which residues in interface should be designed or not. or what types of mutations are allowable

Would it be a serious problem if I want to NOT use resfile? for example, I worry  about disturbing protein structure completely due to  too many mutations

design raf rac.txt1.69 KB
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Tue, 2019-05-28 07:04

I don't see any problem with trying the script as-is, first (without a resfile).  This should result in one side of the interface being designed, the other being repacked without design, and all 20 amino acids being allowed at all designable positions.

After examining the output, you might find that thare  are pathologies that you could correct either with a resfile or by modifying the script (e.g. too many or too few hydrophobic residues, too many glycines and alaniens, _etc._)  But as a first pass, I'd recommend trying the script without modification to see what happens.  It's easier to address problems when you know what they are!

Tue, 2019-05-28 13:24

thanks for your response I have another question


I want to design interface of a complex which contains only alpha helices ( has not any betta strand) , it is important for me that the secondary structures of alpha helices would not be disturbed during sequence design.

Recently I have found a suitable mover  '"AddHelixSequenceConstraints Mover"

 I think by using this mover during interface design  some constraint in sequence design cause to preserve the secondary structure of  alpha helices during design

Now I have two questions first does this mover do what I want? 

and second, did I add this mover to my script in the correct place? would I add or edit something in my script ? I have attached my script here

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Thu, 2019-05-30 23:46