[Dock-fans] protein-protein docking and sphgen

John Irwin jji at cgl.ucsf.edu
Tue Apr 5 18:19:35 PDT 2005


Hi Sebastien

> I am mainly interested in using DOCK for protein-protein 
> docking and was curious as to whether there are any sites 
> providing in depth instructions as to how to do this using 
> DOCK or whether there is anyone out there that can offer 
> advice. The DOCK documentation doesnt discuss macromolecular 
> docking in much detail. I am also curious as to how succesful 
> DOCK is in such situations and how it compares to other 
> programs for macromolecular docking.

This lab has published protein-protein docking using DOCK (below), but it is
not a current research project. For more info on protein-protein docking,
take a look at http://capri.ebi.ac.uk.

Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple
residue conformations and residue substitutions. Protein Science 11,
1393-1408 (2002).


> I was also wondering whether there are any alternatives to 
> using the sphgen program. Is sphgen only available as F77 
> code (as oposed to other languages)? Is there anywhere I can 
> find more information regarding its license? 

Sphgen comes included with UCSF DOCK. What is the problem you are having
with sphgen?


Is the algorithm 
> described in the Surface Solid Angle-Based Site Points for 
> Molecular Docking paper
> (http://helix-web.stanford.edu/psb98/hendrix.pdf) available 
> online or still being researched/developed? And finally are 
> there any other similar alternative molecular shape descriptors?
> 
> I am new to the group and any help would be greatly 
> appreciated. I am an honours student at Sydney University 
> attempting to use DOCK for my project.
> 
> thanks,
> Sebastien Gerega
> 
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