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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 

Dear Sir or Madam,

previously I have always downloaded Rosetta with binaries. But for now the Rosetta package with binary files became too huge (over 17 GB), which makes the Rosetta package download through slow browser (1 Mbps in average and it doesn't depend on a browser) really complicated deal. Other problem, which complicates downloading the Rosetta package, consists in that, what the download process is aborted when laptop screen fades and laptop go to sleep mode.

I know that rosetta_scripts XML protocols can be run in PyRosetta, and I think there is also a specfic PyRosetta version of fastDesign.  But I'm wondering to what extent the underlying functions used in fastDesign (e.g. modifying constraint strengths, modifying vdw repulsion terms) can be written in PyRosetta directly such that some customization would be possible?

Hello

Which application is suited for increasing affinity between 2 proteins? I would like to specify ranges of residues to be mutated in only 1 of the proteins/chains, e.g. in a resfile. 

Essentially I want to do something like the opt-dG application in RAbD, but with ranges of residues a protein domain that is not an antibody. Can the opt-dG do this?