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Structure prediction

Comparative Modeling Templates for Protein with Multiple Domains

Submitted by Morrian_Lynn on Wed, 2020-03-04 10:42
Category: 
Structure prediction

I want to build the structure of a protein that consists of multiple chains. One of my templates is homologous to the entire protein, but the other templates are only homologous to portions of the protein. I found an early post that suggests manually merging different structures into a sequence that's homologous to the entire protein. Since this answer was posted in 2012, I wonder if is there any new approach to deal with structures that are homologous to different parts of the target?

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Rosetta 3 - Applications

Are 100 structures the maximum generated when using homology_with_end_extension (broker protocol)?

Submitted by thaisarns on Fri, 2020-02-21 05:46
Category: 
Structure prediction

Hi!

I have one protein that I would like to model ab initio the final 29 residues (1 - 160 is fixed/I have the x-ray crystallography model,  161 - 189 is the region to be modeled).

I am using the following parameters:

- protein.tpb

CLAIMER RigidChunkClaimer

REGION_FILE protein.region

PDB_FILE protein.pdb

END_CLAIMER

- protein.region

RIGID 1 160 0 0 0

- the command I ran :

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Rosetta 3 - General

FARFAR2 error

Submitted by lijunnju on Tue, 2020-02-11 08:09
Category: 
Structure prediction
Nucleic Acids
ROSIE

Hi ROSIE and FARFAR2 team,

       I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.

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ROSIE - General

error: Unable to open weights/patch file in using ddg_monomer.linuxgccrelease

Submitted by xinmiaohe on Thu, 2020-01-30 22:09
Category: 
Structure prediction

 

 

Dear Friends and experts

I am trying to use "ddg_monomer.linuxgccrelease". First I want to pre-minimize the structure and get mincst.log file. I put all options in a flag file called pre_minimize

I run the following command:

/home/jy/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/minimize_with_cst.linuxgccrelease @pre_minimize

1. To pre-minimize, the command from protocol is as following:

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Rosetta 3 - Applications

Protein-Protein Docking or Comparative Modeling

Submitted by Morrian_Lynn on Wed, 2020-01-29 19:01
Category: 
Structure prediction
Docking

I found a structure of a binary protein complex and tried to use it as my template to predict the combined structure of another 2 proteins. In this case, should I use the protein-protein docking protocol or the comparative modeling protocol?  If I should use the protein-protein docking protocol, is there anyway for me to utilize the PDB file of the template structure to save me some work? And if I should use comparative modeling, how can I build a structure by inputting 2 queries? I assumed that homology modeling only deals with one input query?

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Rosetta 3 - Applications

Centroid mode minimization

Submitted by Martin Floor on Tue, 2020-01-21 07:34
Category: 
Structure prediction

Hi everyone,

I was wondering if there is something like the Relax Application but to use it directly in centroid mode. I know AbInitio uses fragment insertion to start building structures in centroid mode that are later fed to the All-Atom relax application, but is there something that can do a montecarlo local exploration without leaving centroid representation?

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Rosetta 3 - Applications

Error of compiling AbrelaxApplication.cc

Submitted by ylwang on Wed, 2020-01-01 19:12
Category: 
Structure prediction

Hi,I want to use ResolutionSwitcher in Montecarlo.cc to relax pdb after stage1-4,when i add "#include<protocols/abinitio/ResolutionSwitcher.hh> in MonteCarlo.cc",it turn to be a error"Resolution switcher was not declared in this scope".

I included all the header files but still not working.

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Rosetta 3 - Build/Install

What is the best protocol to predict the missing residues in X-ray crystallisation?

Submitted by lanselibai on Sun, 2019-12-29 04:44
Category: 
Structure prediction

I know the full amino acid sequence for my protein. I have obtained its X-ray crystal PDB structure, as well as the mtz file from the crystallisation. There are several loops and termini not resolved. Can I ask what is the best protocol to predict the missing part? I understand it would still not be fully "true" after Rosetta's modelling. I just want to have a "mostly likely" one that can be used as the starting point for my molecular dynamic simulation.

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Rosetta 3 - General

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