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Dear all,

I have just started out my work in a computational protein design lab.
The first algorithm I learned at the beginning was backrub, which I know basically could be used for flexible backbone design.
After using it for a while, I have some doubt in my mind.
Would you mind sharing your valuable experience on the following situations regarding backrub?

1) I have generated 50k structures by backrub.
After removing redundant sequences, the number of unique amino acid sequence was just 1k.

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro. Thanks in advance

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Hi There,

Myself Haresh, I am postdoctoral fellow at University of Toronto. I used PyRosetta for protein protein docking and working good. Usually rosetta did protein protein doking between only two proteins. Is there any avaiblity or options to do protein-protein docking with bound ligand with each protein(e.g. Protein-Ligand --- Ligand-Protein)? Thanks in advance for your help.

Looking forward to hear from you.  

Hi, I am now trying to do an ab initio structure prediction with the constraint information generated from Gremlin.

My script of ab initio structure prediction with Rosetta is as follows, with the part related to constraint data bolded: