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Replacing a single residue in a structure

Submitted by Wexter300 on Sat, 2023-09-16 14:23
Category: 
Design

I have a structure i have been working with for a while, and I wish to replace the last residue in the sequence with a cysteine. I have tried to write a xml script that would perform the spot mutation, but I could not figure it out. Is there a specific rosetta function or way to perform spot mutations? I have also considered just manually replacing the residue with cysteine, and relaxing the structure through rosetta, but i'm not sure if the cysteine would stay in the sequence.

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Rosetta 3 - General

FixedBB design output no beta strands

Submitted by tkoh on Fri, 2023-08-25 01:02
Category: 
Design

I am attempting to use the rosetta FixedBB design application to investigate possible conformation changes that may occur given a single point mutation whilst taking into account romaters. However, as an initial run of the application I do not change any residues or rotamers as I just want to see how this application works, but the resulting output differs from the input structure in that the beta sheets are not visible when visualized.

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Rosetta 3 - Applications

Error when using published constraints file

Submitted by Delfosse57 on Thu, 2023-08-17 11:22
Category: 
Design

Hello,

I am attempting to follow a recent publication released by the Baker group. I am using this cst file to constrain an iron atom to a histidine:

https://github.com/ikalvet/heme_binder_design/blob/main/theozyme/HMM/HMM_His.cst

I have renamed the HMM residue to match with my ligand name.

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Rosetta 3 - General

PyIgClassify cannot renumber and label CDRs my Nanobody-Antigen complex for RabD

Submitted by WBNeT on Fri, 2023-07-07 10:58
Category: 
Design

Hi,

I've been trying to use the Anibody Designer but i was unable to use PyIgClassify webserver to renumber and label the CDRs in my PDB file. I am also unable to get it to find CDRs in any antibody pdb file even thoughs its within the database. I would also like to find the schema for how the CDRs are marked within the text of the renumbered PDB file. Any help would be appreciated.

 

Thanks,

Will

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Rosetta 3 - Applications

non-zero ddG of binding even without mutations

Submitted by top-gun98 on Wed, 2023-06-07 17:19
Category: 
Design

Hello,

I was trying to work with the "calculate protein-protein ddG" tutorial. The tutorial comes with a resfile for mutating an Alanine with Tryptophan at residue 98. Following the steps gives, I get a ddG value of -6.6533 REU.

However, when I replace the line "98 D PIKAA W" with "98 D PIKAA A" (i.e. esentially replacing the alanine with alanine), I'm still getting a ddG value of 6.6643 REU. Can anyone point out why I might be getting a non-zero ddG even though I'm not even 'mutating' the proteins.

Regards,

top-gun98

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Rosetta 3 - Applications

Changing amino acid profile while keeping the backbone conformation between 2 protein structures (need help)

Submitted by seamoon on Wed, 2023-05-24 07:46
Category: 
Design

Hello, i am a masters student trying to play around with rosetta. And i have a project in mind. I have two protein structures: nanocages. each with 60 monomers but the chains are a little bit different with different aa profiles. Now what I want to do is to make a structure with the backbone conformation profile of one of the nanocages but with the amino acid profile of the other one. How do i go about doing this? I'm sorry if I wasn't clear english is not my native language. 

Thanks for your help in advance. 

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Rosetta 3 - General

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