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Structure prediction

RosettaCM: help to generate similar models as those from Robetta Server

Category: 
Structure prediction

Hello,

I have a query protein with 300 amino acids and I want to predict its homology models based on the template (saying templateA.pdb) with exactly same 300 amino acids (for testing purpose).

By using Robetta Server, what I did was listed below:

I pasted the query target sequence, and I selected comparative modelling option and set 1000 models.

I then uploaded the template PDB structure (templateA.pdb).

Post Situation: 

How RosettaCM can perform part of C terminal domain (CTD) structure prediction without proper template structures (coordinates)

Category: 
Structure prediction

Hello,

I want to know in RosettaCM (or Robetta Server), how to generate the C terminal domain (CTD) coordinates where this query CTD domain has no corresponding template structures?

Here is the example:

>Query_Fasta

VVPRRKAKIIRVRQEDEDEDE

>Template_Fasta

VVPRRKAKIIRVRQ-------

Post Situation: 

RosettaCM: adding constraints while keeping AUTO constraints

Category: 
Structure prediction

Hi all,

I am working on the structural prediction of a symmetric multidomain protein using RosettaCM - I have to add a tetramerization domain for which no template structure is available, but for which I can set some distance constraints to steer the prediction in the right direction. For this, I changed

Post Situation: 

Compile C++ Rosetta to Pyrosetta ERROR

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Compile C++ Rosetta to Pyrosetta ERROR

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Compile C++ Rosetta to Pyrosetta

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Compile C++ Rosetta to Pyrosetta

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Fewer than expected structures in clustering output

Category: 
Structure prediction

Dear community,

I am running structure prediction of a protein whose tertiary structure is unknown. I use the standard abinitio protocol explained in the Rosetta tutorial(s). I have currently generated 3000 decoys, which I tried to cluster in order to have an idea of which structures were mostly populated.

Using the following command for clustering:

cluster.default.linuxgccrelease -in:file:fullatom -cluster:radius 3 -nooutput -out:file:silent ./cluster.out -in:file:s *.pdb 

Post Situation: 

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