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Structure prediction

JobDistributor problem in antibody modeling

Submitted by Wizard on Wed, 2015-04-22 00:35
Category: 
Structure prediction

Hello everyone,

I build Rosetta 2015.12 on Scientific Linux 7 (SL-7). And, I follow the protocol of RosettaAntibody3 to do antibody modeling. 

(https://www.rosettacommons.org/docs/latest/antibody-protocol.html)

When, I run the script of “antibody.py” through following command as

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Rosetta 3 - Applications

Repeatability of DDG calculation

Submitted by jennifer on Wed, 2015-04-08 05:29
Category: 
Structure prediction

Dear all,
I have been trying to run a theoretical alanine scan on a protein.

Unfortunately, I cannot repeat the results I obtain when I run exactly the same experiment (just copy all files to a new directory and run again) more than one time. Attached is a png of the correlation between run 1 and 2. The black line is 1:1 correlation. You can see that some mutants look ok (green ring) while others are very badly different (red rings).

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Rosetta 3 - Applications

Total score problems with high-res ddg_monomer

Submitted by jklesmith on Tue, 2015-03-10 15:54
Category: 
Structure prediction

Good Afternoon,

I'm running the high-res protocol of the ddg_monomer on a 439 residue enzyme structure (following the the Kellogg paper and online docs protocols) and I'm seeing some odd score outputs.

There are three types of odd outputs in the ddg_predictions.out file:

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Rosetta 3 - Applications

Floppy tail: sidechain mutation during calculation

Submitted by syoifczeri on Mon, 2015-03-09 19:01
Category: 
Structure prediction

Hello

Recently, I am trying to predict flexible tail region of protein by using Floppy tail.

First I tried to use Floppy tail with test data (4tailstestdata.pdb).

I have run Floppy tail as below command

mpiexec -np 4 FloppyTail.mpi.linuxgccrelease -in:file:s 4tailstestdata.pdb -in:file:movemap mapmover -nstruct 4

//movemap
RESIDUE 90 117 BBCHI
RESIDUE 207 233 BBCHI
RESIDUE 324 351 BBCHI
RESIDUE 441 468 BBCHI

and I got 4 pdb files those file and each model has different amino acid sequence.

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Rosetta 3 - Applications

ddg_monomer: How the ddG is actually calculated based on the 50 trajectories? What scorefunction is used?

Submitted by lanselibai on Tue, 2015-02-24 02:38
Category: 
Structure prediction

(relevant files can be downloaded at https://copy.com/yOhxRslZzK8j9z0l)

Dear friends,
In the instructions about ddg_monomer,

https://www.rosettacommons.org/docs/latest/ddg-monomer.html

it is mentioned that "the most accurate ddG is taken as the difference between the mean of the top-3-scoring wild type structures and the top-3-scoring point-mutant structures".

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Rosetta 3 - Applications

Access to latest CS-ROSETTA tools

Submitted by smg3d on Fri, 2015-02-13 13:57
Category: 
Compilation
Structure prediction
Fragment Generation

Have been trying to access the latest CS-ROSETTA tools without success for several days. Looks like www.csrosetta.org has been down for a while.

Any alternative to www.csrosetta.org to access latest cs-rosetta tools?

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Rosetta 3 - Build/Install

minirosetta: how to reserve (inter-chain) disulfides after relax ?

Submitted by lanselibai on Sat, 2015-01-24 10:56
Category: 
Structure prediction

(I would appreciate it very much if any of my questions can be answered.)

Dear friends,
I have been trying to reserve the disulfides of my target protein during the minirosetta comparative modelling. However, though I have gone through many posts, I still could not work it out after using several disulfide related flags.

My situation is:

in the target protein:
Light chain (LC): residue 1-214
Heavy chain (HC): residue 215-442

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Rosetta 3 - Applications

force field, energy function

Submitted by masterofpuppets on Wed, 2015-01-21 11:06
Category: 
Structure prediction

Hello everybody,

I am interest in, which force field Rosetta use and which energy functions are applied for a normal abinitio calculation. If I used an abinitio calculation with a metallatom, are there used a other force field for the zinc atom?!
Can anybody advice my a good paper which an easy explanation or something like that?!

many regards

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Rosetta 3 - General

FloppyTail as a rosettascripts file

Submitted by tiagogomes89 on Mon, 2015-01-19 02:45
Category: 
Structure prediction

Hello rosetta community,

I was wondering if anyone has a RosettaScripts xml file that emulates de FloppyTail application. I´m currently generating decoys of a two domain protein
with a big disordered linker with the objective of modeling it to saxs data.
I just wanted to gain more control over the process and to see exactly what the application is doing.

Thank you,
Tiago

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Rosetta 3 - Applications

How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?

Submitted by lanselibai on Sat, 2015-01-17 11:19
Category: 
Structure prediction

Dear friends,
I have a Fab (antibody fragment of antigen binding) with two chains(LC 1-214, HC 215-442). An interchain disulfide bond is supposed to form between LC-214-cysteine and HC-434-cysteine. I am using 4KMT as its homology template. In the 4KMT structure, the interchain disulfide bond does exist. However, after replacing the residues with my own residues, the interchain disulfide bond has lost and become "-SH" instead of "-S-S-".

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Rosetta 3 - Applications

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