Design

Hey everyone,

I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.

Hi,

I'd like to model one of the histidines in my structure to be in a protonated form with hydrogens on the NE2 and ND1.  I see there's a param file for protonated histidines (~/rosetta/database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states/HIS_P.params).  What's the best way to specify in my pdbfile that I want that particular histidine to be protonated?

 I tried renaming the residue to "HIP" in my pdbfile and changing the first few lines of that param file to be:

I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.

It always complaints:

hi all,

I am working on protein design for antibody-antigen complex to improve the binding affinity. so far, I have the crystal structure of the antigen (chain A) and the antibody Fab (chain H and L). now I want to re-design part region of one CDR loop (around 5 residues) involved in direct interaction to antigen. besides the design for the loop retaining original length (5 AA), I also try to make the loop shorter or longer with the randomizing the residues of loop.

any suggestion that where I can start from?

many thanks,