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Enzyme Design

Converting all residues to poly-Gly/Ala

Submitted by jtpi6174 on Tue, 2023-05-09 14:14
Category: 
Enzyme Design

Hey, I am pulling my hair out over this. I am trying to convert all residues in a protein to poly-Gly/Ala (for example 1ae1.pdb) but cannot find the Rosetta function to do so. I am replicating a paper where they included code and output, the output appears to be typical Rosetta output (the .pdbs are like 3tzc___1.pdb) which I am assuming were generated with a Rosetta function.

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Rosetta 3 - General

Which application/mover should I use to evaluate the ddg between apo enzyme and enzyme binding with transition state?

Submitted by JasonIsaac on Wed, 2023-02-22 18:36
Category: 
Enzyme Design

Hi everyone:

        I used Enzyme Design application to get a series of enzymes with ligand(transition state of my target reaction). Now I want to inspect the free energetic change upon the protein transition state binding. 

        So I first look into the ddg_monomer application, and I find this application is suitable for comparing ddg energy between wild-type protein and its mutant structures. This can't meet my needs.

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Rosetta 3 - General

De Novo backbone generation vs Rosetta Match for enzdes and ligand binding.

Submitted by csvajda on Thu, 2022-06-30 09:55
Category: 
Enzyme Design

Howdy Yall, 

So I have not been in the Rosetta world for very long, and most of what I have learned I have had to parse from the Rosetta Commons Demos/Documenation and various publications since no one else at my institution does this sort of work. So while I have learned quite a bit, there is some fundamental questions about approach/methodology that I feel blind towards.

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Rosetta 3 - General

How to use 'CYZ' residues?

Submitted by Seongsung on Fri, 2022-06-03 01:40
Category: 
Enzyme Design

Hi, all.

 

I want to refine a PDB file with one zinc ion using 'SetupMetalsMover'.

 

I have added one zinc ion which is predicted to coordinate with cysteine and histidine.

I noticed there is 'CYZ.params' file and 'residue_types.txt' file ( '/database/chemical/residue_type_sets/fa_standard/residue_types.txt' file ) includes the 'CYZ.params'.

Then, I changed the residue name of cysteine to 'CYZ' (from CYS).

And then, I executed rosettascript to refine my pdb.

 

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Rosetta++ - Applications

Disulfidize- "Extra content at the end of the document"

Submitted by ldlamini on Tue, 2022-05-17 02:37
Category: 
Enzyme Design

Hello all!

I'm attempting (my first attempt) to use the disulfidize mover to predict disulfide bridges across a monomer of of homo-oligomer, this is the exact example on the tutorial.

I get this error "Extra content at the end of the document". I have run the the XML rewriter script on my .xml file  and there appears to be no issues.

I've attached my script. I'l appreciate any insight.

Thanks in advance

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Rosetta 3 - Applications

Rosetta Matcher not recognizing protonation forms of CST files like CYZ, HIS_D, etc

Submitted by Hirbond on Tue, 2022-03-01 13:16
Category: 
Enzyme Design

Hi All,

I am using Rosetta 3.9 from the TACC for my Matcher run and want to use alternative protonation states of the amino acids I am working with, such as deprotonated cysteine CYZ or delta-Nitrogen-protonated histidine, His_D. Rosetta already has these residues defined in its database but Matcher can't recognize them at all. Does anyone know how I could approach this problem?

 

Thanks for the help in advance!

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Rosetta 3 - Applications

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