[Dock-fans] protein-protein docking and sphgen
jji at cgl.ucsf.edu
Tue Apr 5 18:19:35 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.
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,
> 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
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.
> Sebastien Gerega
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