Inserting residues using RosettaRemodel
Submitted by eleishaj on Tue, 2015-11-24 08:54
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Design
Fixing part of a ligand in dock-design
Submitted by hssnzdh2 on Mon, 2015-11-23 17:14
Category:
Docking
Design
Hi,
I am using a dock-design protocol to design a binding pocket to bind a ligand. I know where parts of the ligand should bind (orinetations and the position in protein) but the other parts can be flexible. Right now after the dock and design protocol, most of my outcomes change the whole position of ligand and don't keep that part fixed. Is there a way to tell the program to keep parts of the ligand fixed? or a way to generate conformers for only parts of the ligand?
Thanks.
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Protein/Protein Ddg demo: How to write predicted mutant structures?
Submitted by cossio on Wed, 2015-11-04 20:14
Category:
Structure prediction
Design
I am following the protein/protein Ddg demo:
https://www.rosettacommons.org/demos/latest/public/calculate_protein_protein_ddg/README
I am wondering if there is a way to modify the script mutation_script.xml so that I can write the predicted structures of the mutants to PDB files?
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What is "repack", "prepack"?
Submitted by cossio on Wed, 2015-11-04 17:59
Category:
Structure prediction
Docking
Design
All over the place in Rosetta Documentation, I find the terms "repack", "prepack". But I have not found their definitions. I suspect that "repack" and "prepack" refer to conformational samplings where only amino acid side chains are moved, while the backbone remains fixed, but I can't be sure. Is it in this sense that these terms are used here?
What are the definitions of "repack" and "prepack" (in the common usage of these terms in the ROSETTA community)?
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pose.replace_residue() & incorrect scoring
Submitted by msun on Tue, 2015-10-06 10:51
Category:
Design
Scoring
Hi developers,
I wasn't sure where to submit bug reports so I'm posting here instead.
I've noticed a scoring error after repeated pose.replace_residue() function calls. The final pose after repeated calls to replace_residue() ends up having a score substantially lower (often < -50 Rosetta energy units) than when scored using the scoring application or if the pose is loaded upon application initialization.
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fixbb algorithm reference?
Submitted by tylerborrman on Wed, 2015-09-23 10:20
Category:
Design
Hi,
I'm interested in understanding how the fixbb application works. It mentions in the documentation page:
https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d4/d68/fixbb.html
a stochastic simulated annealing approach is used. However, I do not see a description of this approach in the references on that page.
I did find a reference to a Metropolis Monte Carol procedure here:
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ERROR: Rosetta does not recognize the property: SIDECHAIN_THIOL, when running minimize_with_cst.linuxgccrelease
Submitted by cossio on Thu, 2015-09-03 08:46
Category:
Design
This is the command I am trying to execute (taken from here: https://www.rosettacommons.org/docs/latest/application_documentation/ana..., in the Preminimization of the Input Structures paragraph, in High Resolution Protocol):
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loop modeling
Submitted by bharat_46010 on Thu, 2015-08-06 01:34
Category:
Design
Hi,
I am trying to mutate the residues of a loop using resfile but it seems that the rosetta doesn't read the resfile at all. I checked this by adding a random sentence and ran the job, which ran perfectly but with native loop sequence. Here are the options which I used for loop modeling:
flag file:
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Peptide building
Submitted by berk on Thu, 2015-07-30 06:53
Category:
Design
Hi Dear Rosetta Users/Developer
I have 1000 3-mer peptide sequence like as GSH, SAD, GPN, PWW, ...
Now, I would like to build them in a fast way using Rosetta scripts.
Would you please advise me on how to do it?
I will be grateful for any help.
Best,
Berk.
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score:weights for fixbb application in Rosetta 3.5
Submitted by tylerborrman on Tue, 2015-07-28 14:16
Category:
Design
Hi,
If you specify a weights file using the option '-score:weights' , will that weighted scoring function be used in optimizing side chain placement? That is, does the simulated annealing algorithm incorporate the scoring function specified by '-score:weights', or is 'score:weights' only used in the final scoring of the structure AFTER side chains are placed and the designed PDB is complete?
Thanks,
Tyler
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