[Dock-fans] protein-protein docking and sphgen

Sebastien Gerega sger3477 at mail.usyd.edu.au
Tue Apr 5 17:04:30 PDT 2005


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.

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? 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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