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Enzyme Design

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

mp_transform optimize with franklin2019 scoring

Submitted by benhardy on Thu, 2020-05-28 08:35
Category: 
Design
Scoring
Enzyme Design
Membrane

Hi All,

I am running some flexible backbone design on a transmembrane four-helix bundle heme protein via RosettaScripts. I'm finding that the membrane residue is moving a lot during design, and I have to optimize the embedding with mp_transform post-design to reposition the mem residue. I have a few questions about this:

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Rosetta 3 - Applications

protein relax

Submitted by Alison_Yajie on Tue, 2020-05-19 08:29
Category: 
Enzyme Design

I am trying to relax my protein with ligands FMN before do further design. I used movemap to exclude the rotamer on FMN. my flag and movemap file looks like below. I also attached my protein_FMN pdb. It takes an extremely long time and it seems like stuck somewhere (I attached the screen shot). Is it normal and anybody knows why? Thanks

flag file:

-in:file:s ./input/3TX9.A_FMN_Crystal.pdb

-in:file:movemap movemapfile

# Harmonic runs

-relax:constrain_relax_to_start_coords

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