Hi Andreas, This maybe a little ott, but the Rosetta suite of modelling programs will do docking with some minimisation and side chain optimisation. You can also enforce symmetry.
http://www.rosettacommons.org/ http://depts.washington.edu/bakerpg/ It is free to academics and runs on most platforms. Hope this helps, Dave On 29/11/2007, Andreas Förster <[EMAIL PROTECTED]> wrote: > > Dear all, > > Karen question reminded me that I have one also. > > I study a protein that homodimerizes via a long helix. A number of > homologs exist. They all dimerize, but the structure is only known of > the first. Homology is high enough that I can easily thread the > homologs' sequences onto the structure. > > How do I go about analyzing the new dimerization interfaces? Before > having Pisa have a go, I'd like to do some sort of minimization to allow > for wiggling of one helix with respect to the other and rotamerization > of side chains. What I'm ultimately interested in is which homologs are > likely to form heterooligomers. There is some experimental evidence for > that. > > I'm grateful for suggestions. > > > Andreas > > -- > >> Andreas Förster << > Imperial College London > https://wasatch.biochem.utah.edu/~andreas > -- ============================ David C. Briggs PhD Father & Crystallographer http://personalpages.manchester.ac.uk/staff/David.C.Briggs/ AIM ID: dbassophile ============================
