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Docking

DNA-protein docking

Category: 
Docking
Nucleic Acids

I didn't find any contemporary comment on that so I'd like to ask about how to dock protein structure to dsDNA in Rosetta? Is that possible now anyhow?

I have small protein structural motif, like HTH and try to model its interaction with a sequence within dsDNA to get some hints about which residues will bind to which DNA bases so I don't have to scan along huge DNA strands but rather have a well-defined location within the major groove to explore.

Thanks for all advice.

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my status jobs been queued in such longer time

Category: 
Docking

Hi there,

I saw most status of daemon showed [DEAD]. I had sent multiple jobs using peptiderive methods. However, till now my jobs still in queue listing. What happened actually in there? stuck?. Please response this email as soon as possible. I need these data info to make up my article. Here in my list of jobs:

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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 

 

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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,

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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).

 

 

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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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