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FloppyTail vs. Remodel for linkers

Submitted by attesor on Mon, 2014-07-07 08:36
Category: 
Design

I have a 11aa long linker (known sequence) connecting two parts of a protein (NOT two independent domains). I want to model the linker before some downstream Rosetta analysis on the protein. It seems FloppyTail is often suggested for the modeling of linkers.

My question is: how is FloppyTail compared to Remodel + Fixbb? What if I just insert some 11aa long extension (of any sequence) between the two parts using Remodel, then I use fixbb to mutate this newly inserted extension to the sequence of my linker? How would this compare to FloppyTail?

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Rosetta 3 - Applications

Failed glycine check when running RosettaRemodel to build disulfide

Submitted by cheyuk on Fri, 2014-06-27 02:31
Category: 
Design

Hi Rosetta users,

I was recently running RosettaRemodel to build a disulfide between two residues. The first residue is a gly and the second is tyrosine. I ran into this error:

"Failed glycine check. Cysteines cannot replace glycine positions in the native pose."

Is this because gly doesn't have a CB atom so that the CB-CB distance cannot be measured? I can think of mutating the gly to other residues as a workaround. But is there any other way to build a disulfide bond involving a gly using RosettaRemodel?

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Rosetta 3 - Applications

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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Rosetta 3 - Applications

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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Rosetta 3 - General

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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Rosetta 3 - Applications

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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Rosetta 3 - General

How do I explicitly add residues for design in the interface optimization script?

Submitted by ahonegger on Mon, 2014-05-12 07:40
Category: 
Docking
Design

I am playing around with the interface optimization script in the demo "design_raf_rac_interface" (rosetta3.5). For the system I am working with, I would like to add a few residues to the list of residues to be redesigned, an not redesign all residues of the interface, but only those around a mutated residue in the binding partner.

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Rosetta 3 - Applications

Connecting linkers

Submitted by Prasanth Kumar on Tue, 2014-05-06 00:53
Category: 
Structure prediction
Design

Hello,
I plan to design a small protein fragment using flexible linkers (to connect the breaks) out of a larger protein.
Using which rosetta application i should use to put the residues of the flexible linkers to get the complete 3D structure of the shorter protein.

Please Help me!
Thanks in advance
K.Prasanth

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Rosetta 3 - Applications

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