June 15, 2016

The folder haddock0102 contains a rigid body docking simulation of the SOX9 dimerization 
region, modeled as one amphipathic helix (termed helix a0), onto the helix a1 and a2 of 
the SOX9 HMG domain. 

Following a typical HADDOCK protocol, the directory is populated with the command 

   haddock new.html
   
The run1/run.cns script was only modified to use the CNS version on a laptop. 

The run1/run.cns script uses 'AIR' type ambiguous restraints between the a0 helix and the
a1/a2 HMG platform (distances/ambig.tbl) and some hydrogen bond restraints to maintain
good helical geometry (hbonds/hbonds.tbl). 

200 structures calculated in structures/it0 were analyzed an the 20 lowest energy selected
in structures/it1. The 20 structures were categorized based on the orientation of helix a0
on the HMG domain as shown in the Supplementary Material.

Logan Donaldson / logand@yorku.ca
