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Loop Modeling

[dev] quickest way to determine bond distance between polymeric-bonded residues in Pose/Conformation

Category: 
Loop Modeling

Hi,

I'm trying to determine the bond lengths between consecutive residues in a Pose/Conformation, to determine whether they are actually close enough to be bonded, or if there is a gap between the residues that needs to be closed or filled in. Is there a straightforward way to do this?

Thanks

Post Situation: 

-loops:fa_input not found in command line top-level context

Category: 
Loop Modeling

Hi everybody!

I'm trying to learn how to use Rosetta in de novo protein design. I use this article as a manual: https://www.ncbi.nlm.nih.gov/pubmed/23744289

It doesn't work for me at some point. Namely, when I go to step 13 (Running the comparative modeling job), I try to execute the following command in the terminal:

./loopmodel.default.linuxgccrelease @modeling.options -database rosetta_database -nstruct 100

But the response is:

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Cyclizing .pdb of a linear chain.

Category: 
Loop Modeling

I am trying to take a .pdb structure that I generated (of a non-canonical peptoid backbone) and cyclize it in order to conduct GenKIC analysis and find favored configurations.

I tried creating the residues with PeptideStubMover, but the coordinates were considerably out of place, such that a given residue was connecting atoms several angstroms off and at angles that made no sense.

I am now trying to work with a premade .pdb structure, link the N- and C-termini, then use an .xml to set up the GenKIC rules.

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domain:domain fusion

Category: 
Design
Loop Modeling

Dear all

I would like to insert a domain at the N-terminus of protein and at the same time build different linker sizes. Which application is the best suited? My impression is that domain insertion protocols, like remodel, broker or AnchoredPDBcreator, assumes that we are not at the end or a protein. Is there a way to do this?

thanks in advance

best

felipet

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Adding centroid .params files for non-canonical residues based on all-atom .params files

Category: 
Loop Modeling

On the matter of using GenKIC to model a loop of noncanonical groups like beta-peptides or peptoids, the GenKIC program falters due to lack of centroid data.

The requirements for centroids is confirmed by removal of the ALA.params file from: database/chemical/residue_type_sets/centroid/residue_types

This causes the same error as it does for sequences of beta-peptides and peptoids for which there are all-atom params files in: database/chemical/residue_type_sets/fa_standard/residue_types/

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How to add a residue to one chain of an existing structure?

Category: 
Loop Modeling

Hi,

I have a structure. I do homology modeling of another target. The template has a peptide of length 9. The new target that I am modeling has a peptide of length 10. When I perform the modeling, the target misses that 1 residue of the peptide. Is there a way to add that residue to the end of peptide?

I tried various things:

1. Adjusting the alignement (this always messes up something) before using rosetta_cm.

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Loop modeling/closure for many structures

Category: 
Loop Modeling

Hi,

I am trying to do homology modeling. I thread around a thousand structures. Before performing the energy minimization, I want to identify broken structures and  stitch them. What are the possible ways to do it? So basically,

1. I want to identify those structures that require loop modeling (broken structures)

2. Perform loop modeling on all those (say there are a couple of hundred structures).

3. Then perform energy minimization.

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Domain insertion with Non-CAA

Category: 
Design
Loop Modeling

Hi all,

I am trying to insert a long fragment (GFPStrand) into another protein (4e1s) using Remodel. I've delete the residues that were originally in 4e1s but left a few at the end as an anchor for the domain insertion. Remodel throws an error about insertion indices being 0 if I don't leave them to anchor it. Remodel accepts the domain insertion and starts on the loop closure. It also appears to close the loop, but then throws this error with trace: 

Post Situation: 

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