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.

 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

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.

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.