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Structure prediction

Using residue patches in AbinitioRelax

Category: 
Structure prediction
Chemically Modified Residues

I am hoping to 'fold' short phosphorylated peptide sequences, and started by generating fragments with SS predictions on the unphosphorylated peptides. For example, I ran this sequence through a local installation of PSIPRED and picked 200 3- and 9-mers:

>1
MKGDAHRYLAEFATG

I checked that the TYR_p:phosphorylated patch was active in the full-atom patches.txt, then created a centroid patch and added it to the patches.txt by analogy to existing patches:

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Predicting the part of protein strcutrue

Category: 
Structure prediction

Hi,

I have a protein whose sequence is fully known and whose structure is partial known. Most sequences of the protein are folded in the luminal ER domain and this part is resolved by experiments. However, transmembrane and cytosolic parts of the same protein are not resolved. As only the luminal part of the protein is resolved, I would like to predict the structure for transmembrane and cytosolic domains. Is there a way to predict only these parts while I keep the experimentally-resolved luminal domain?

Thanks, Siyoung

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RosettaAntibody core.pose.util error

Category: 
Structure prediction

Hi,

I'm using Rosetta 3.8 on Linux (rosetta_bin_linux_2017.08.59291_bundle; pre-compiled binaries). I'm trying to use the RosettaAntibody3 workflow as documented here, but am running into the following error when I run the sample command (using the sample antibody sequences in antibody_chains.fasta as given in the workflow):

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Iterative local rebuilding vs automated structure refinement

Category: 
Structure prediction

I've been using the iterative local rebuilding approach based on this tutorial: 

https://www.rosettacommons.org/demos/latest/public/electron_density_structure_refinement/structure_refinement

In a recent publication titled "Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta", the following was mentioned:

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KIC with fragments versus Next generation KIC

Category: 
Structure prediction

Dear all,

I wanted to pick your brains. I am using KIC with fragments to modell a loop. I am under the impression that this protocol outperfromrs the next generation KIC. Could you confirm this for me and perhap refer me to the relevant paper? Is the KIC with fragment protocol better?

Alternatively, can I use the KIC with fragments protocol with the flags from next generation KIC?

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