How can move peptide on cleft of enzyme on Flexpepdock?
Submitted by phanvy on Thu, 2014-06-05 02:22
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Problems with fixbb in Rosetta 3.5
Submitted by mdidonato on Wed, 2014-06-04 13:56
Category:
Design
Hello,
I am trying to run fixbb on a heterodimeric protein and explore different residues at 2 different positions in one chain. The program runs without error however all the structures output (100) have the native residues at those 2 positions. My .resfile and flags are below.
Resfile:
NATRO
EX 1 EX 2
USE_INPUT_SC
START
72 A NOTAA C
79 A NOTAA C
Flags
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question about the exposed strand results in beta_strand_homodimer_design demo
Submitted by szypanther on Wed, 2014-06-04 00:47
Category:
Design
Dear developer,
I follow the tutor to run the beta_strand_homodimer_design demo, i wanna use the method to design the EGFR dimmer,
In order to confirm the reliable of rosetta, i download the 1IVO.pdb (Crystal structure of the complex of human epidermal growth factor and receptor ) from the PDB database and then edit the pdb file directly. I just keep one of the ERBB1 structure as the active ERBB1 receptor after deleting the others in the homodimer .
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Docking protein complexes when constrained by oligomer symmetry
Submitted by msk on Tue, 2014-06-03 11:09
Category:
Docking
I am currently trying to set up a docking run between two proteins that have compatible symmetry, and almost certainly interact along a 3-fold symmetry axis. One molecule is trimeric, the other is a D3 hexamer, with protomeric MWs of 20 and 25 kDa respectively. I have experimental (x-ray) structures for both proteins, and an initial model where the two proteins are in contact, and lined up with the 3-fold axis of each along Z. I therefore want to search only rotations around Z, along with a small Z-translation shift.
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ProteinLigandInterfaceUpweighter for protein-protein interactions?
Submitted by ahonegger on Mon, 2014-06-02 06:53
Category:
Design
In the selection of binders from a library and their affinity maturation, a trade-off between affinity of the binder and its stability frequently can be observed. Starting from a binder library based on a very stable framework allows for high sequence diversity in the randomised positions of the putative binding site, and therefore stringent selection for high affinity, as very significant destabilisation would be needed to bring the stability of the binder down to a level where this stability significantly affects the fraction of folded molecules and therefore the outcome of selection.
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why can't I find the folder of "main"? Did anybody succeed in using phenix.rm_rosetta?
Submitted by aini1314 on Sat, 2014-05-31 05:28
Category:
Phenix / MR Rosetta
I found someone had solve a difficlut proble by combine the rosetta with phenix, which can help calculate the x-ray structure with low resolution.
http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2648.html
http://link.springer.com/article/10.1007%2Fs10969-012-9129-3
So I want to copy this as well to solve my problem, and I found a way to combine rosetta with phenix. Here is the website about phenix.rm_rosetta:
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a question about protein-ligand docking in generating 1SW2 conformers
Submitted by Ryhon Wang on Wed, 2014-05-28 22:27
Category:
Docking
Hii everyone,
I am looking forward in prepareing 1SW2 ligand structures using rosettaligand arls package. I don't generate ligand conformers in this case,
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Error 500 Docking protein
Submitted by Sherpaman on Tue, 2014-05-27 01:32
Category:
Docking
Dear all,
I have submitted a couple of protein-protein docking (docking2) jobs.
I have received the confirmation mails but the results aren't accessible, even if i can see them in my queue list as "Finished". I Suppose they are not failed aas i would expect a "Failed" status, but i got this "Error 500 - We're sorry but we weren't able to process this request." reply.
How can I fix it?
Thank you
Andrea Coletta (Sherpaman)
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error when running beta_strand_homodimer_design
Submitted by szypanther on Sun, 2014-05-25 20:22
Category:
Design
Hi All,
I encounter a series problem when running this demo, and past my questions as follows:
(A) About the README file problem, At the second step, I think the command is not right, Is the "@finder_option" should be replaced with "@maker_options" ?
2) Make the potential homodimers
There are two ways to do this. If you are only doing it for one structure is is easy just to use this command line
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Creating model of 89-90 residues by ab initio methodology-help
Submitted by krlitros87 on Sun, 2014-05-25 12:12
Category:
Structure prediction
Dear rosetta users,
This is my first time using ab initio modelling in order to obtain a protein's structure (though i have some experience on comparative/homology modelling).
I'm trying to obtain the structure of 2 proteins of 89 (COR15A) and 90 (COR15B) residues respectively. Sadly i can't use the homology-modelling methodology because i don't have a proper template to use it.
Anyway, i have already built 100 structures of one of my protein (COR15B) by using the following command:
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