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Enzyme Design

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

enzyme design and scoring function

Submitted by rohi on Fri, 2021-06-25 10:29
Category: 
Enzyme Design

Hello,

In enzyme design, the scoring function is enzdes.wts. Do we need to change it to the most recent scoring function (ref2015)?

Also, is SR_*_interf_E_1_2 the binding energy? can we say this score is related to specificity of an enzyme?

 

any suggestion is appreciated.

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Rosetta 3 - General

Recommendations for CoupledMoves enzyme redesign

Submitted by dgm3 on Thu, 2021-03-04 10:53
Category: 
Enzyme Design

I'm preparing to start an enzyme redesign project using Rosetta, but the paper I'm supposed to be working off used the older enzdes application, which doesn't seem to be compatible with newer scorefunctions and sampling methods. CoupledMoves seems preferable, and I was hoping to get some recommendations for putting together a ligand docking and design protocol. I have basic familiarity with Rosetta, but since I'm the only person in my lab using it right now, I'd really appreciate any advice to help speed up the process and reduce time spent on trial and error.

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Rosetta 3 - General

WindowsError: [Error 32]

Submitted by jetu20 on Sun, 2020-10-11 21:02
Category: 
Enzyme Design
PyRosetta

I am trying to use IntearctiveRosetta on windows 10 environment and have zero knowledge about coding.....could anyone help me to solve this error......which comes up when I do a position scan using IntearctiveRosetta.....

Traceback (most recent call last):File "scripts\daemon.py", line 2024, in daemonLoopdoPMutScan()File "scripts\daemon.py", line 503, in doPMutScanos.rename("scanprogress", "scanoutput")WindowsError: [Error 32] The process cannot access the file because it is being used by another process

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PyRosetta - General

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