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How to use MHC Epitope energy (mhc_epitope) to deimmunize a protein structure?

Category: 
Design

Dear all,

The MHC Epitope energy (mhc_epitope) alogrithm  (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/MHCEpitopeEnergy) is for deimmunization of epitopes. However I cannot understand how to use it. 

I used the pdb file 2b3p.pdb and the score controlling script in the introduction webpage as the inputs and run the following command:

Post Situation: 

core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

Category: 
Design

Dear developers,  

I tried to follow the antibody design protocol from the Nature protocol articles but unfortunately I keep getting the following error when I try it:

core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

This is my command line: 

antibody.default.linuxgccrelease -ignore_unrecognized_res -fasta antibody_chains.fasta

and this is the content of  ROSETTA_CRASH.log:

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antibody.mpi.linuxgccrelease some antibodies failing to model

Category: 
Design

Hello all, I am using the antibody.mpi.linuxgccrelease to model multiple antibodies. Most work fine but about 10% are failing with weird error messages.  I have tried everything to figure out the problem but am having no luck. These antibodies are clinical molecules, and so I feel like my failure rate is pretty high, and I'm probably doing something wrong.  There is not a lot of documentation about the (newer) antibody homology modelling application and so I am a little bit at a loss as what to do to make the program more robust. Thanks as usual for all your help!!!

Post Situation: 

location of define_interface.py

Category: 
Design

Hello,

I am following the protein design steps presented in the Dr Mieler lab. One of the steps is to generate resfile with  define_interface.py script. I checked my rosetta/tools/protein tools/scripts path, but there is not such a file. Where can I find this script?

Thank you

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Help with filtering (Rosetta scripts)

Category: 
Design

Hello

I'm running running a pilot ROSETTA script to get the GreedyOptMutation mover with the ddg filter to work. But I get this error message;

ERROR: ERROR: No acceptable mutations found. All possible mutations failed at least one filter!

Any ideas on how to get the filter to allow trajectories with mutations that improve ddG and increases affinity between the 2 proteins contained in the .pdb?

My .xml looks like this:

 

<ROSETTASCRIPTS>

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RosettaRemodel gives no increased output when setting higher -num_trajectory

Category: 
Design

I am trying to design a helical linker between two strongly interacting subunits that connects their termini using RosettaRemodel.

I am running remodel with the following flags in mpi mode and get the desired output (around 2-4 structures with -num_trajectory 32). However when I increase -num_trajectory to e.g. 1000 I still get only around 2-4 strucures out (named 1.pdb 2.pdb ...). while computation time increases drastically.

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Pepspec Anchor Dock

Category: 
Design

Good evening, I want to use the pepspec anchor dock application and I am using the following flags file:
-ignore_unrecognized_res
-pepspec :: no_prepack_prot
-pepspec :: anchor_type PRO
-pepspec :: prep_align_prot_to input / 1CKA.nopep.pdb
-s input / 1CKA.nopep.pdb
-pepspec :: ref_pdb_list input / homol.pdblist
-restore_pre_talaris_2013_behavior
-score :: weights pre_talaris_2013_standard.wts
-pepspec :: soft_wts soft_rep.wts
-pepspec :: interface_cutoff 6
-pepspec :: n_dock_loop 1

Post Situation: 

multi state protein design

Category: 
Design

Hello,

I have an enzyme and I want to optimize its sequence to increase its binding to one protein and decrease its binding to another protein at the same time. I recently attended Rosetta workshop and learn about multi state protein design which can be used to increase affinity of an antibody to its ensemble of antigen, but I am not sure whethe it is applicable to my case. I would appreciate any suggestions.

Post Situation: 

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