Hi Jerry,
I've not got a whole lot of experience with docking programs but I have
used 3D-dock (http://www.sbg.bio.ic.ac.uk/docking/) to do docking trials
between two proteins and found it to be easy to set up and use. It uses
an algorithm that mainly looks at surface complimentarity between the
two proteins but it helps a lot if you use some biological information
to restrain the results.
Hope this helps,
Ronan
Jerry McCully wrote:
Hi, All:
Recently we solved a complex structure between two proteins,
which indicated the interaction was kind of
rigid.
Therefore we want to test the binding mode of the receptor with
another homologous ligand(very similar structure, RMSD 2.4 angstrom).
Can somebody recommend a sophisticated docking program to do this?
Thanks a lot.
Jerry McCully
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