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Structure prediction

Structure prediction using true distance and angle constraint

Category: 
Structure prediction

Hello,

I wonder if naive protein structure can be predicted by using true distance and angle constraints.
If we can do that, how do we choose rosetta applications and parameters?

Post Situation: 

antibody protocol fails

Category: 
Structure prediction

Hello,

I'm using antibody protocl to graft some models but it fails with the following error:

File: src/protocols/antibody/grafting/chothia_numberer.cc:152
ERROR: Unxpected length of light-fr3 [length=31], length expected to be: [32, 33, 34]!

Do you have any comments on this? I have three sequences (three different antibodies with light and heavy chains) and it works on one of them but the same error on the two others.

Thanks a lot in advance,

Best

Post Situation: 

A problem with "make_fragments.pl" script dependencies

Category: 
Structure prediction

Dear fellows,

I would like to generate fragments for protein sequence structure prediction ab initio locally, on my laptop, without involving any server, such as Robetta. I carry out it with a help of make_fragments.pl script. And I met with several problems with make_fragment.pl dependencies. I want to solve these problems. Could you advise me, if you can, how to solve them, please?

My first problem consists in follows:

Post Situation: 

PDB file name too long to be handled by file system

Category: 
Structure prediction

Hello,

in ddg_monomer module, we have encountered a problem with the length of the PDB file name when predicting mutant with 50+ mutations. Since Rosetta constructs the PDB file name based on the mutations included in the predicted mutant as prefix + list of mutations, with a large number of mutations this file name can be longer than 255 characters which causes the file system to be unable to store the PDB file. Is there any way how to prevent this behavior, for example set rosetta to store PDB file under user given name? Thank you for you answer.

Post Situation: 

Ab initio structure prediction for long amino acid sequence

Category: 
Structure prediction

Hi

I'm a postgraduate student, interested in protein structure prediction.

I noticed that the document said:

  • Abinitio: max 150 amino acids are cosidered possible

So, I want to know, how to use rosetta to predict number of protein of  amino acids more than 150 (e.g. 500)?

Post Situation: 

FARFAR2 structure prediction give a circular RNA

Category: 
Structure prediction

i have suplied Farafar2 with an RNA sequences of length 47. the server returns a complete circular structure. i dont have a template and am just giving the fasta file. when i give the dot-bracket structure along with the fasta file, it returns an error too.  

Post Situation: 

IS there any source code about protein structure prediction with only sequences information?

Category: 
Structure prediction

Hi,

     I see the server Robetta and I want to know is there any source code ? I download the rosetta source code but fail to find the function about this part?

     Wish your help

Post Situation: 

De novo structure building with medium resolution map

Category: 
Structure prediction

Dear all,

I am trying to build a model for my protein and I have a medium resolution map (~5-6 A). I tried backbone tracing manually, but many regions are dubious. This protein does not have any homologous protein either, so I am looking for tools to do denovo model building with guided electron density. Is there any available protocol to achieve this?

Best,

Buddy

Post Situation: 

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