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Enzyme Design

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

Enzyme design gets 0 hit

Submitted by cryosky on Sun, 2021-09-26 13:24
Category: 
Enzyme Design

Hi,

I'm doing a de novo design of an enzyme to fit in a new molecule. There is a protein structure papers that proposed the interactions between another molecule and residues in the protein and I found two molecules share the same atoms in these interactions. So I transfer these interactions and written them into the cst file. There are a total of 3 blocks. However, I found the program reports 2000+ hits after the first round but 0 hits after the second round. What's causing this error and what should I do to get more hits?

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Rosetta 3 - General

Rosetta Enzyme design cst block raises error

Submitted by cryosky on Thu, 2021-09-16 08:47
Category: 
Enzyme Design

Hi All,

I'm trying to run the Rosetta Enzyme Design protocol and I wrote a cst file for the matching step.

My cst file includes two blocks (I pasted below), they use the exactly same format but when I add the second block the match program starts to report an error.
 

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Rosetta 3 - General

clashes created with enzdes

Submitted by listofdina on Mon, 2021-08-02 06:51
Category: 
Enzyme Design

 

Hello, 

I'm working on de novo enzyme design. Utilizing the enzdes application through theozyme definition. While doing regular design procedures I have noticed that Rosetta inserts amino acid identities that create clashes with the ligand. Most notable is an Ile with a distance of 3A to the ligand, instead of the minimum 4. Images attached. As far as I know, I have not altered the default behavior of vdw radii at any point.  The energies for these residues do not sky-rocket and Rosetta scores these designs very favorably.  

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Rosetta 3 - Applications

Problem with match on enzdes

Submitted by ahuls1 on Thu, 2021-07-29 13:21
Category: 
Enzyme Design

Hi all! I am attempting my very first enzyme design campaign and running into issues with matching. I generated a cstfile from averaging native pdb measurements within a family, and am trying to match my theozyme (a new substrate - LFF) to one representative structure as a test (PDB ID: 5nci chain A).

When I run:

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Rosetta 3 - General

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