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Rescoring regions of structures

Submitted by erin_cutts on Mon, 2013-07-22 04:43

I am working on structure prediction of a protein that is predominately unfolded and I have used rosetta (csrosetta actually) to do prediction. While my clustering looks good, ie conserved features in the protein are clearly visible, I can't get funneling plots due to loop regions ruining the score. It seems to have 5 unstructured residues at either end, and a 5 residue loop. I want to rescore structures based on the regions that are similar, such that when I plot rmsd vs score I have the best hope to see funneling for the folded region of the protein.

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Rosetta 3 - General

how to add water into protein interface using solvated rotamers?

Submitted by chinhsutran on Sun, 2013-07-21 20:25

Hello,

Im new to Rosetta. Im trying the tutorials of PyRosetta, but I couldn't find any clues that could help me add water into the protein interfaces using the Solvated Rotamers (as stated in the paper by Jiang et al. 2005 "A solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces).

Anyone please suggests me any hint or readings that I can find how to do it!

Thank you very much.

Regards,
chinh

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PyRosetta - General

add water into protein interfaces using solvated rotamer?

Submitted by chinhsutran on Sat, 2013-07-20 07:33

Hello,

Im new to Rosetta. Im trying the tutorials of PyRosetta, but I couldn't find any clues that could help me add water into the protein interfaces using the Solvated Rotamers (as stated in the paper by Jiang et al. 2005 "A solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces).

Anyone please suggests me any hint or readings that I can find how to do it!

Thank you very much.

Regards,
Chinsu

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PyRosetta - Scripts

A problem with RosettaLigand

Submitted by Rosettasz on Fri, 2013-07-19 16:09

Hello, everyone,

I just started to learn Rosetta, and was wondering if I could get some help here.

I was trying to follow the Ligand Docking example which was used during the Workshop held in April this year .
While the protocol was done with rosetta3.5, I am using rosetta3.4.
And I got some problems during the run.

I prepared the following files as instructed:

receptor: 2Q5K_mutant.PDB
Ligand: SAQ_aligned.pdb
Ligand conformers: SAQ_conformers.pdb
Ligand parameter file: SAQ.params
Water: water.pdb
XML file: water_dock.xml
option file: options.txt

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Rosetta 3 - Applications

Loop prediction

Submitted by yzhou on Thu, 2013-07-18 14:24

A protein is composed of N and C domains.
In the experiment, the protein was cut into these two domains and each of them was solved by crystallography.
However, the structure of the loop linking these two domains was unknown.
Therefore, I hope to predict the loop structure so that it can link the solved two domains.
How to achieve this goal?
Look forward to the reply.
Thanks.

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Rosetta 3 - Applications

Unsatisfied interface H-bond in Ligand docking

Submitted by Prasanth Kumar on Thu, 2013-07-18 12:04

I am leaning docking with 3dau. I followed the documentation: I went to docking after repacking the cofactor using ligand_rpkimin and then appended the ligand cofactors.

~/rosetta-3.4/rosetta_source/bin/ligand_dock.linuxgccrelease -database ~/rosetta-3.4/rosetta_database/ -s 3dau_aligned_plus_nap_plus_mtx.pdb -in:file:extra_res_fa ~/Desktop/docking_3DAU/NAP.params ~/Desktop/docking_3DAU/MTX.params -ex1 -ex2 -ex1aro -nstruct 1 > out.log

I got something interesting in the log; But there were NO errors or warning:-

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Rosetta 3 - Applications

high-res docking

Submitted by tfliu on Mon, 2013-07-15 02:49

Category:
Docking
Hello:
After low-res docking,I'm going to do high-res protein/protein docking.There are two modes(High Resolution Docking Only;High Resolution Docking minimization)in the rosetta3.4 user guide.Which one should I choose?
Here is my flags:
1.High-res docking only flags
-s 1.pdb

-partners ABC_DE

-ex1

-ex2aro

-use_input_sc

-docking_local_refine

-nstruct 1000

-mute core.util.prof

-out:overwrite

-out:pdb

-mute core.io.database

2.High-res docking minimization flags
-s 1.pdb

-partners ABC_DE

-ex1

-ex2aro

-use_input_sc

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Rosetta 3 - Applications

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