AutoDock
AutoDock Work in Progress
Testing the side chain flexibility in AutoDock
4.0
We have now added side chain flexibility to
AutoDock, and we are now in the process of testing this.
Mutable atom types for de novo molecular
design
We have been investigating mutable atoms in
the design of linkers in DNA minor groove-binding drugs.
Protein flexibility using discrete maps and
averaged maps
We are currently testing two methods for the
incorporation of limited protein flexibility into AutoDock: a discrete
map approach, and an averaged map approach. Both require a collection of
known structures that adequately sample the conformational space of the
protein.
GUI for setting up parameter files and launching
dockings.
Ruth Huey has been developing a GUI (graphical
user interface) that helps in setting up AutoTors, AutoGrid and AutoDock,
and in launching and monitoring distributed docking jobs. It is called
"AutoDockTools" or ADT for short, and we are now distributing
it. This has been built on top of Michel Sanner's Python Molecular
Viewer, or PMV.
And there's more...
But that would be telling... : )
AutoDock