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Dimeric interface redesign

Category: 
Design

Hi all,

I would like to redesign the dimeric interface using the heterodimer structure of protein A and protein B. I searched several protocols and saw how to increase affinity or stability by fixing one of them and changing the other. However, I want to increase the binding affinity between the two proteins by changing both sides at the dimeric interface. Anyone know how to do that? Has this method been tried before? If there are papers or protocols that I can refer to, please let me know.

Any help will be very appreciated.

Best,

Post Situation: 

Correctly Formatting a PDB file for analysis of a Zinc Finger Motif

Category: 
Compilation

I have been trying to correctly format a zinc finger motif for docking in RosettaDock-3.2, but have apparently failed after many efforts.  I have attached the PDB file.  The zinc is located within Chain A and coordinated by residues within Chain A.

Post Situation: 

about “protein mimic designer”

Category: 
Design

Hi everyone, has anyone used the program protein mimic designer? I imitated the article "De novo design of potent and selective mimics of IL-2 and IL-15" to design IL-2. In the first step, I got a lot of pdb files and stored them in the folder 01_results_scaffoldsMimicsIL2/debug. I I don't know if this result is correct, because there is an error at the end of the program running: segmentation fault (core dump).
If anyone has done it, what is the result of your first step?

The results of my first step

Post Situation: 

please help in compliation Rosetta on Ubuntu 20.04, extras=hdf5!

Category: 
Compilation

hello,everyone! I ran into a problem when I complied rosetta with option "extras=hdf5". I have installed hdf5 in /usr/local/hdf5,  and I have add it to environmental variables.

command line: ./scons.py -j16 bin mode=release extras=hdf5

results:

Post Situation: 

Question about remodelling

Category: 
Design

I am new to Rosetta. And we hope to redesign a protein and let it easier to dock with another two protiens.  Hope to verify if my approach is correct here.

Step 1) I applied the Rosetta protocol - remodel and create the blueprint file by "~/rosetta/main/tools/remodel/getBluePrintFromCoords.pl"

Step 2) Edit the blueprint file and apply the commands ALLAAxc to all residues. 

Post Situation: 

Cannot login ROSIE-2 (docking-3)

Category: 
ROSIE

Hi,

When I tried to log in to Rosie (Docking-3), it requires logging in to my Github account, however, it always come up with the following message (please see the attached picture). In fact, my GitHub account (email address) has been verified already, but it still comes up with the same error message. How can I deal with issue? Is this because of the missing institutional domain? I'm from Mcgill University, could you add my institutional domain: mcgill.ca? 

It would be highly appreciated if you reply to me earlier.

Thanks

Post Situation: 

Residue outside res_map range

Category: 
Docking

Hello,

I have been trying to dock a ligand into my protein but I am getting two different errors. The first time I ran sbatch launch_design.sh and it would time out and give the files pocket-183006.err and .out, but the out file was empty. I tried running multiple jobs by creating a new file RosettaDesign.sh but it would fail, and I got the files pocket2-198770.err and .out. The error I received is residue outside res_map range. I have uploaded the files in text form and was wondering what is causing it to fail.

Post Situation: 

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