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GeneralizedKIC side chain closure.

Submitted by almeida85 on Mon, 2022-09-19 06:13
Category: 
Design

Hi all,

I want to generate cyclic peptides in a binding site employing the anchor design approach similar to https://www.nature.com/articles/s41467-021-23609-8 and  https://www.pnas.org/doi/suppl/10.1073/pnas.2012800118. I need to do the closure by amidation between two side chains (K/E) or side chain/C-terminal.

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Rosetta 3 - General

Proper indexing of grafted residues by CCDEndsGraftMover

Submitted by cttm4a1 on Wed, 2022-09-07 23:41
Category: 
Design

I found that the grafted residues by CCDEndsGraftMover do not have proper indexing. They have no chain ID, and all residue numbers are 0. If the XML option copy_pdbinfo was set to 1, the grafted residues just shared the same chain ID and residue number as the original segment. I am wondering if there are any movers that do the following tasks.

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Rosetta 3 - General

Sequence symmetry during FastDesign for repeat protein design

Submitted by cttm4a1 on Tue, 2022-09-06 21:02
Category: 
Design

I want to design a repeat protein that self-assembles into a designed structure. As a result, I want each repeat to acquire the same sequence after the FastDesign mover. Is it possible that during FastDesign mover, all repeats are mutated the same way? Is there any Taskoperation (or mover) I can call to set up such a constraint?

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Rosetta 3 - General

Get fasta from PDB script correction - Solved

Submitted by ialvy on Tue, 2022-08-30 00:00
Category: 
Design

Dear researchers,

Those who really want to use the get_fasta_from_pdb.py script to generate the FASTA files from PDB, generally face some sorts of errors.

The most common error is: TabError: inconsistent use of tabs and spaces in indentation

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Rosetta 3 - General

Unrecognized D-Leu name / C-terminal ACE

Submitted by almeida85 on Thu, 2022-08-11 07:43
Category: 
Design

Hello,

I am designing a macrocycle with simple_cycpep_predict that contains a D-Leu in the N-terminal and an acetylated ASP in the C-terminal. My sequence_file (-cyclic_peptide:sequence_file) is DLE ........ ASP

1) When I run the app it doesn't recognize the D-Leu name:

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Rosetta 3 - General

Nanobody design

Submitted by chandana on Tue, 2022-08-09 20:36
Category: 
Design

Hi everyone,

I am trying to design a nanobody using an available antibody. After grafting heavy chains from an antibody to a known nanobody scaffold, and aligning with the antibody-antigen complex structure, I obtain nanobody-antigen compelx structure. I am trying to use Rosetta design to increase its affinity to antigen as well as sample possible new CDR sequences using the options,

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Rosetta 3 - Applications

simple_cycpep_predict - Design mode - The base name "ARG" was added more than once

Submitted by almeida85 on Thu, 2022-08-04 02:57
Category: 
Design

Hello,

I am using simple_cycpep_predict in design mode to find derivatives of a peptide for disulfide cyclization. For the -cyclic_peptide:allowed_residues_by_position option I am using the following file:

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Rosetta 3 - Applications

RIFdocking：Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/

Submitted by sia on Tue, 2022-08-02 20:06
Category: 
Design

Hello, everyone, I encountered some problems when I was doing Step 19: Actual motif grafting of RIFdocking.
First, I need to turn my scaffolding into a silent files. The command is as follows: 

cat scaffolds.list | silentfrompdbsparallel > scaffolds.silent

After the command is run, I got the following error:

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Rosetta 3 - Applications

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