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Docking

Protein-Protein Docking or Comparative Modeling

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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appropriate sampling for protein docking to a multi chain assembly

Category: 
Docking

Hi,

I want to locally dock a 10 kDa protein A in the middle of a 4-subunit protein assembly (BCDE, ~50 kDa each). I roughly know the orientation of A on the BCDE platform, where A contacts every other chain. After placing A near its target binding site I first run relax -nstruct 5 and use the 'best' model for a subsequent full local docking (A_BCDE) with rosetta scripts (linuxgccrelease v3.7). I am getting reasonable energy funnels (both I_sc and total score vs. RMSD) with -nstruct 50, but I wonder if my sampling scale is appropriate for the task.

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using DARC in rosetta

Category: 
Docking

 

 Hi all

  I'm using DARC(Docking approach using ray-casting) to do the blind ligand docking.

  In the tutorial of DARC, to include electrostatics calculations,  tools from openeye such as omerga were used.

  tools in openeye are not free.

  Are there similar tool or program to do electrostatics calculation in DARC  which is free?

 Thanks

Regards

 

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using piper-flexpepdock

Category: 
Docking

 

 Hi

 I want to try the blind peptide docking with PIPER-Flexpepdock in Rosetta application

In Rosetta manual, it is written that 3 algorithms are there in Flexpepdock and one of them is PIPER-Flexpepdock.

But in downloaded rosetta package, I couldn't find it in main/source/bin

Where can I find it ?

or to use PIPER flexpepdock should I do something in build/install step?

Thanks

Regards

 

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Docking the border segments of coiled coils in parallel orientation

Category: 
Docking

Dear Sir or Madam,

I need to dock the border segments of two coils (from four ones) from each of two homotetramers in a parallel orientation (I mean, that docked helix bundles should lay in one direction).

I would like to find out, which kind of files should I use and/or parameters in that files should I write for docking these segments in a proper way?

I will be sincerely grateful for your responses and advises and I am looking to it.

Best regards,

Corvin.

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Docking Metalloprotein-Protein

Category: 
Docking

hi all

I try to dock one metalloprotein (ZN and Ca) to a small protein inhibitor.

I started, as suggested in the session “Working With Metalloproteins in Rosetta”, relaxing the crystal structure of the metalloprotein applying the flag -in:auto_setup_metals, in the full atom mode.

The relaxed structure and protein inhibitor were added to the same pdb file (at 20A of distance )and used as starting coordinates to the docking protocol.

 

The problem was in the Centroid Docking Phase, I guess.

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change number of output pose files written out (default=50) in ligand docking XML script

Category: 
Docking

Using the Rosetta docking tutorial XML script as a reference, see below, how can the number of output pose files be changed? It seems there is a default of 50 files set somewhere but unfortunately I cannot find where to overwrite it and can't seem to find any references to it online. I suspect there is a trivial answer to this and I'm just missing the obvious.

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Speed problem when running RosettaLigand ligand docking

Category: 
Docking

Hello, I am trying to do protein design using a protocol derived from RosettaLigand ligand docking.

When I run Rosetta Design as the following command line, everything seems correct and there are output structures (pdb files). The problem is that it takes ages to get the results. In average, it will take 15~20 mins to get one models. For 1000 models, it spent 9 days. I think there is something wrong, but I don't know how to solve it.

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