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Structure prediction

Comparatively modelled chains are far apart in final structure while the template pdb has all chains in a close-knit complex

Category: 
Structure prediction

I tried to model a protein sequence (4 chains) using RosettaCM. The structure of the protein is already available in PDB (2ERJ). The issue I am facing - the final modelled structure has all the 4 chains very far apart, unlike the pdb. What exactly is going wrong? 

I am obtaining the alignment file from Clustal omega. The target fasta sequence is given as chain1/chain2/chain3/chain4 and the 2ERJ fasta is also given in the same format in clustal omega so that the final alignment has only 2 unique identifiers in the ali file, like this:

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Membrane Abinitio modeling error

Category: 
Structure prediction

Hi,

I am modeling a 178 residue membrane protein sequence using the abinitio protocol

To briefly describe what I have done:
1. generate structure fragments using Robetta server
2. generate a span file using OCTOPUS server and the script, octopus2span.pl
3. generate lipophilicity prediction file (.lips4 file) using run_lips.pl

4. generate PDB using membrane_abinitio2.linuxgccrelease

I can run the BRD4.fasta in the tests successfully following above protocols.

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Extracting PDBs from a Silent file: "Can't find residue type for ARG"

Category: 
Structure prediction

Hello everyone,

I am refining protein structures into Cryo-EM maps, and my output is a silent file. Currently, I am attempting to extract the pdbs from the silent file so that I can analyze and score the structures. The protein has a missing loop, and it is failing on the C-terminus right before the missing loop. Specifically, my error for each structure is "ERROR:  can't find residue type for ARG:CtermTruncation at pos 114 in sequence G". 

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not knowing which one of three ways to run rosettascript

Category: 
Structure prediction

Hello,

I meet a question when I am to run rosettascript. I found three executables but I do not know which one to choose. I am wondering whether some one can help me out. I would be much appreciated. 

I found three ways, as below, to run rosetta scripts I am wondering what are differnece in these three executables. Will they give same results for the same inputs. whether settings are same in these three ways. 

rosetta_scripts.default.linuxgccrelease 

rosetta_scripts.linuxgccrelease

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RosettaCM or FastRelax?

Category: 
Structure prediction

Hi,

I have a Cryo-EM density  and AA sequence for a protein , but the density  is not good enough for assign the residues unambiguously.

I'm particularly interested in one alpha-helix and based on secondary structure prediction, I have roughly known the AA sequence for the helix.

But the secondary structure prediction can't tell the boundary of the helix unambiguously.

Could anybody have any ideas about how I can get the correct register for the helix using Rosetta???

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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).

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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-------

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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

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