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protein protein interaction design

Category: 
Design

 

Hello

I have docked two proteins  and Now I am going to design the binding interface of one of them while fix everything in the other. I mean I want to do protein protein interaction design. which part of rosetta would be for this job?? is it fixbb?

 

 

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How to use the <CavityVolume> filter in the released version of Rosetta

Category: 
Design

I am trying to replicate the work of the paper entitled "De novo design of potent and selective mimics of IL-2 and IL-15”​.

However, I get the following error when I run Rosetta Script (Rosetta 2019.14) with deNovoPreprofiledMimeticsDesign_gen2.xml:

Error messages were:
From line 38:
Error: Element 'CavityVolume': This element is not expected.

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loop design for Conformational bias

Category: 
Design

Hi

   I have a protein with two domain connected by short loop.  depending on ligand and post-translational modification, it adopt open or close conformation. I want to design the loop residues so that I can shift the equilibrium towards close conformation.  what is the best way/protocol to do that in Rosetta?

 

Thank you

Dhiraj

Post Situation: 

error in peptiderive job result

Category: 
Design

I am submitting the job correctly as shown in the sample data. The pdbid that i am submitting has only one chain, as in the original protein structure. The chain that is present has the catalytic site, binding site. Still the error after the job completion says resubmit or check that the pdbid should have two or more than two chains, so i tried submitting another protein pdbid, which has two chains, still the error shows same display. 

Hoping for the help from your side as early as possible.

Thankyou.

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How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?

Category: 
Scoring

Hi, I am doing the design of a batch of decoys.

I want to block the designs of residues 1-9 and residues 80-91 for all the pdbs.

However, some of the pdbs do not have certain residue numbers (e.g. pdb1 has missing residue number 1, pdb2 has missing residue number 82).

May I know how to specify residue numbers so I can still use a single resfile for the whole batch of pdbs?

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Choosing weight file for interface design?

Category: 
Scoring

Hi, I am now trying to do an interface design of a nanobody docked to the target (through its CDRs, by patchdock).

I have some doubt about choosing the best weight file for scoring of the designs. May I have some suggestions from you?

Actually, I have read from here and I have already learned that:
1) Choose score weighting by finding what was used for the most similar application in published literatures.

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Memory leak when PDB preparation

Category: 
Scoring

Hi everyone,

   I am preparing the pdbs from pdb.org for scaffold. About more than 6000 pdbs were downloaded and have been preparing. However, the memory leak was encountered. I have try to use -linmem_ig 10 and -jd2:delete_old_poses to resolve the problem. But the memory leak is still there. 

Could you help me to solve this problem?

   Thanks a lot.

Post Situation: 

How to determine the value size in block of *.cst files?

Category: 
Design

HELLO, everyone,

I am a begineer of Rosetta de nevo peotein design and want to design an enzyme using rosettamatch, however it is complicated even i have read its method carefully. Recently, I am trying to use demos, and i found that are really helpful and important. But some used files need to be made by hand, such as the *.cst file. The question is how to determine the value size in block of *.cst files to constrain a ligand and residue interaction, including :

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