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Docking

Docking of multichain oligomers

Category: 
Docking

Hi all,

I'm trying to perform docking simulations for two identical coiled-coil homodimers modelled by the fold and dock protocol to establish the potential ways of interaction of these in higher order complexes (there's an experimental evidence for the formation of such assemblies).

 

The command looks as follows:

docking_protocol.linuxgccrelease -in:file:s S_029104.pdb -unboundrot S_029104.pdb -nstruct 1  -randomize1 -randomize2 -ex1 -ex2aro -partners AB_AB 

 

Post Situation: 

antibody_numbering_converter cannot recognize the IMGT scheme

Category: 
Docking

To whom it may concern:

Hi I want to convert my antibody structure from Chothia to IMGT. I use the following command and get an error "ERROR: Illegal value specified for option -antibody:output_ab_scheme : IMGT". I am wondering is the IMGT scheme already cancelled in the number converter program? This is a 2019.35.60890 version.

/home/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_numbering_converter.linuxgccrelease -input_ab_scheme Chothia -output_ab_scheme IMGT -s 1ahw_chothia.pdb

 

Best regards,

Post Situation: 

Error in src/protocols/membrane/util.cc line: 1224

Category: 
Docking

Hi, I am trying to prepare a MPDocking run (v 2019.35).

Both prepacking as well as actual docking crash with the same message:

ERROR: The SpanningTopology object in MembraneInfo is empty!
ERROR:: Exit from: src/protocols/membrane/util.cc line: 1224

However, the attached log file seems to indicate that the molecule was read correctly. Also the TMspans were build and their center calculated (end of logfile).

 

 

Post Situation: 

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?

Post Situation: 

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.

Post Situation: 

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

 

Post Situation: 

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

 

Post Situation: 

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.

Post Situation: 

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