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Loop Modeling

backrub application, resfile, and pivot_residues

Category: 
Loop Modeling

Hi,

I've been attempting to use the "backrub" app to model mutations while allowing flexibility of the backbone in specific protein stretches.

It appears adding the resfile (with or without mutations specified) causes backbone flexibility across the entire output structure and not restricted to the protein stretches specified by -pivot_residues.

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Example:

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FloppyTail options error

Category: 
Loop Modeling

Hello, everyone!

I'm trying to use FloppyTail application, however it always gives me an error:

[ERROR] EXCN_utility_exit has been thrown from: src/protocols/floppy_tail/FloppyTailMover.cc line: 268
ERROR: invalid flexible region (start (0) or stop (0) is undefined) - check your flags or movemap file


I tried to use it with options from the demo (in /integration/tests), and simply running like

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modeling an extracellular loop of a transmembrane protein

Category: 
Loop Modeling

Dear all,

I built a model for a membrane protein and know I try to refine a long extracellular loop using NG-KIC modeling. I noticed that some sgments can reach the outer transmembrane space. I am trying now to use constraints to penalize this behaviour. In your opinion what is the best type of constraints I can use to achieve this.

Regards

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BridgeChainsMover

Category: 
Design
Scoring
Loop Modeling

Hi,

I am using the 2016.28 build and have the some problems with "BridgeChainsMover" from Brian's recent method paper: DOI:10.1007/978-1-4939-3569-7_20

I get this error "ERROR: 'scorefxn' is not a valid option for BridgeChainsMover".  Here is the part of script that returns an error:

<BridgeChainsMover name="connect" chain1="1" chain2="2" motif="3LX-3LA-3LX" overlap="3" scorefxn="centroid_scorefunction" />

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antibody.py

Category: 
Loop Modeling
PyRosetta

Dear all,

I am using the antibody.py script that comes with PyRosetta (rosetta_src_2016.13.58602_bundle, v3.6) and associated software to generate structural models for VH/VL sequences. For most of the sequences that I am using as input, the script terminates at the antibody_graft step with an error (pasted below):

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Loop design with length variation

Category: 
Design
Loop Modeling

hi all,

I am working on protein design for antibody-antigen complex to improve the binding affinity. so far, I have the crystal structure of the antigen (chain A) and the antibody Fab (chain H and L). now I want to re-design part region of one CDR loop (around 5 residues) involved in direct interaction to antigen. besides the design for the loop retaining original length (5 AA), I also try to make the loop shorter or longer with the randomizing the residues of loop.

any suggestion that where I can start from?

many thanks,

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Error in Loop modeling and other queries

Category: 
Loop Modeling

Dear Rosetta users

I have generated a model by fitting a crystal structure to electron density map using flexible fitting software (MDFF). This is a 864 aa long protein with two domains. However I am not satisfied with the fitting of a specific regions( a stretch of ~50 aa between two domains). This region contains a small helix surrounded by loops. I am trying to remodel this region using rosetta loop modeling and using electron density restraints. I am using following flags in the loop modeling protocol-

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CDR Cluster Constrained Relax Equivalent

Category: 
Structure prediction
Loop Modeling

Hi,

Looking through the doucmentation, I found references to an application called "relax_cdrs", which enables relaxation of CDRs with constraints derived from their corresponding CDR cluster.  (link to documentaiton below).

https://www.rosettacommons.org/docs/latest/application_documentation/antibody/CDR-Cluster-Constrained-Relax

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Generating non-redundat dataset for loop models

Category: 
Loop Modeling

Hi there,

I have run two indipendent jobs starting from the same input files except for the seed (ie setting option -jran 1234567 vs. -jran 1234568), in order to produce 1,000 loop models from each jobrun.

Each job is aimed to model simultaneously five loops of more than 14 residue length each one.

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Fusing C-terminal or N-terminal segments onto proteins using Remodel

Category: 
Structure prediction
Design
Loop Modeling

Hi I am trying to fuse a structure onto a designed protein structure at the C-terminus using the following command:

remodel.linuxgccrelease -s model3.pdb -remodel:RemodelLoopMover:bypass_closure -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -num_trajectory 3 -save_top 1 -database <PATH> -overwrite -out:file:scorefile model3.sc

model3.pdb covers the range: 1-393

model4 covers the range: 290 - 393

Where the blueprint has the following general format:

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