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Loop Modeling

GeneralizedKIC disulfide closure

Submitted by Ken on Tue, 2022-08-16 13:32
Category: 
Loop Modeling

Hi all,

I have been banging my head against the wall on this for a while now, and I think it's time to get help.  Here is my problem.  I'm trying to understand how to close loops in a toy example via different residues (head to tail, side-chain/side-chain, disulfide, etc) with GenKIC and I cannot for the life of me understand what the error message is trying to tell me. 

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Rosetta 3 - General

Antigen-antibody modeling

Submitted by aastha.pal on Mon, 2022-06-27 09:34
Category: 
Loop Modeling

I was getting an error while running the snugdock that I solved using the clean_pdb.py command. When I ran flags file using snugdock @flags file, another error came up saying "the antibody doesn't contain start or end of residue of cdr loop H1. Please check pdb is renumbered properly and passed -numbering scheme option matched the PDB.This could also mean missing density in the cdr loop. Loop modeling application can be used to fill missing residues."

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Rosetta 3 - General

genkic mover produced an unwanted HN - CA bond

Submitted by cttm4a1 on Mon, 2022-06-20 14:25
Category: 
Loop Modeling

I ran the tutorial placed in demos/tutorials/GeneralizedKIC/exercise1/ and successfully produced 10 output structures. However, the residue ALA32 that was encompassed by the genkic mover has unwanted HN - CA bond and HN_CB bond. All the 10 output structures have this problem, and I've attached three of them. I tried to FastRelax the strucutre after genkic mover, but the unwanted bonds were still kept.

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Rosetta 3 - General

Modelling at defined pH - for pmutscan - pH:mode not working

Submitted by cagfa1 on Tue, 2022-03-15 04:05
Category: 
Scoring
Loop Modeling
Chemically Modified Residues

Hi all, 

I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.

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Rosetta 3 - Applications

Rosetta (antibody_designer) performance

Submitted by Kihang _Youn on Wed, 2022-03-02 00:48
Category: 
Loop Modeling

 

Hi All,

 

I am building a Rosetta(rosetta_bin_linux_2021.16.61629_bundle) and running the simulation that my customer offerd.

One thing I really want to know and ask you guys is that the performance is okay and how to imporve more.

Here are my environments.

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Rosetta 3 - General

[LoopModelerMover] ERROR: Can't build a fold tree from a loop with an unspecified cut point.

Submitted by dgm3 on Sun, 2021-12-26 18:32
Category: 
Loop Modeling

Hello,

I am trying to use the LoopModelerMover to relax a couple of loops in a protein complex. I would like to let Rosetta select cutpoints automatically so I leave the cutpoints set to 0. An example script is attached as a text file. I have tried specifying the loops as loop subtags and as a loops file, and in both cases I get this error. 

ERROR: Can't build a fold tree from a loop with an unspecified cut point.

 

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Rosetta 3 - Applications

C-termini remodelling of dimeric structure removes second chain

Submitted by LeonhardJS on Wed, 2021-10-13 06:23
Category: 
Loop Modeling

Dear Rosetta Community,

I am trying to remodel a short C-terminal loop into  a docked dimeric structure consisting of 2 identical proteins and while the modeling itself worked, the output contains only the first protein.  The flags I used are the following:
-in:file:s bestp1.pdb
-remodel:blueprint c-term.remodel
-no_optH false
-ex1
-ex2
-remodel:num_trajectory 1
-remodel:quick_and_dirty

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Rosetta 3 - Applications

Linker Building in scFv

Submitted by sam_dc on Sat, 2021-10-09 05:38
Category: 
Loop Modeling

Dear Rosetta Users, 

I would like to build a linker that connects the VH to the VL domain of a single-chain Fv.
The length of the linker is ~15 aa (actually I'm going to build two linkers which differs in term of length).

In the literature, I found a case in which the RosettaRemodel application was used to perform a loop closure with a glycine-serine linker between two domains.

However, the sequence of my linker is known and it must not be changed. 
I just need to build -and not design- the linker.

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