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Installing pyrosetta for proteinmpnn use

Category: 
Design
PyRosetta

What is the best way to install PyRosetta for use with Protein MPNN? I am installing it for myself on an hpc cluster (redhat linux 8) and haven't found much documentation outside of that for the general PyRosetta install.


 

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peptide design

Category: 
Design

Hi, 

I have a protien peptide complex and I want to design a peptide that will bind to the protein better the the WT peptide. What tools do you suggest I use? it can also be from

any of the other rosseta platform (or any other). My goal is to find 50 potential peptides and then test them experimentally.

Thanks, 

Miriam

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Replacing a single residue in a structure

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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FixedBB design output no beta strands

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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Error when using published constraints file

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

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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non-zero ddG of binding even without mutations

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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