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Enzyme Design

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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Rosetta 3 - Applications

Alanine Scanning for 1 Protein (no interface)

Submitted by mags33 on Fri, 2019-10-25 10:08
Category: 
Design
Scoring
Enzyme Design

Hi, does anyone know how to do alanine scanning for just one protein?

I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.

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Rosetta 3 - Applications

"Angle constraint: 0-length bonds" error

Submitted by purvi24 on Sun, 2019-07-28 10:09
Category: 
Enzyme Design

Hi,

I am trying to design the binding site of a protein with certain ligands and there is a common error that I encounter with various ligands (not all). The error says "Angle constraint: 0-length bonds". I checked the input structure and there are no atom clashes. I am not sure what is causing this error. If anyone has an idea, it would be a great help.

Thank you !

Purvi

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Rosetta 3 - Applications

RosettaMatch

Submitted by xingqing326 on Mon, 2019-07-22 13:14
Category: 
Enzyme Design

Hi,

I was trying to run rosetta match with Rosetta/main/source/bin/match.linuxgccrelease   

The match was done successfully with older version of rosetta, but didn't work with Rosetta 3.10. It aborted because of an error of "ERROR: Assertion 'build_sets_[ build_set_id ].restype().has( "1HA" ) failed. ERROR:: Exit from: src/protocols/match/upstream/ProteinUpstreamBuilder.cc line 1210". I was wondering if there's a way to fix this. Many thanks.

 

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Rosetta 3 - Applications

Enzyme Design FlexBB Protocol Bug: DNA/RNA handling

Submitted by kettner on Fri, 2019-06-14 14:16
Category: 
Enzyme Design

Hi Folks,

I've been playing with the enzyme design binary application using enzymes containing DNA or RNA in the pose. The FlexBB protocol can be activated by setting the flag '-enzdes:flexbb_protocol true'. If no loop file is provided via the flag '-enz_loops_file <file>' the default  protocol behavior is to iterate through the pose to identify flexible regions in the structure for loop design. I found that having either DNA /RNA  in the pose triggers the following error consistently after cst minimization. 

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Rosetta 3 - Applications

The question about FavorNativeResidue

Submitted by asbelx on Fri, 2019-04-12 20:02
Category: 
Enzyme Design

 I  read the paper Rosetta and the Design of Ligand Binding Sites doi:10.1007/978-1-4939-3569-7_4.

 

then try to use  EnzRepackMinimize  to design the protein.

But FavorNativeResidue was set as 0.5-3.0, the mutant position numbers are same and there are too many mutant positions.

However, I use the PackRotamersMover  by changing  FavorNativeResidue and can get different mutant position numbers.

How can I solve it? Thanks.

 

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Rosetta 3 - General

Adding bridged water interaction in constraint file

Submitted by purvi24 on Thu, 2019-02-28 07:01
Category: 
Enzyme Design

Hi,

 

I am working on Rosetta Enzyme Design Application trying to design a protein with a particular ligand in desired geometry. I wanted to define a bridged hydrogen bond interaction between the carboxylate group on the ligand and the arginine residue in protein via water molecule.

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Rosetta 3 - Applications

How to minimize only a few key residues' orientation

Submitted by Ronghai Cheng on Mon, 2018-11-05 18:37
Category: 
Enzyme Design

Hi everyone,

I am currently checking mutations of some key residues in the substrate binding pocket. So far, I used pymol wizard to automatically iterate all 20 amino aicds mutations from position and then use rosetta minimizer to optimize the local energy. 

Since I only change a few residues of the protein, is there any ways that I can only minimize a few positions instead of minimization of whole protein?

 

Thanks,

Ronghai

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Rosetta 3 - General

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