ADL: dealing with lots of rotatable bonds ?
j.dyason at griffith.edu.au
Sun Jan 15 20:13:42 PST 2006
I was wondering if I could get some advice on dealing with
molecules with a large number of rotatable bonds. i.e. around the max of
32 for Autodock. I have successfully docked small molecules (only 4 or 5
rotatable bonds using the default autodock (LGA) parameters, except
boosting ga_num_evals to 1,250,000). I am now trying to autodock tetra and
penta saccharides and the results seem to suggest that the conformational
space of the saccharide is not being adequately searched. i.e. it appears
to stay close to a linear shape with no bending to fit the binding site.
>From an article on blind autodocking of peptides (Hetenyi, C.; van der
Spoel, D. Efficient docking of peptides to proteins without prior
knowledge of the binding site. PROTEIN SCIENCE 2002, 11, 1729-1737.) I
tried increasing the ga_pop_size to 250 and the ga_num_evals to
10,000,000. They also suggested a ga_run of 100, I have only tried 10.
This seemed much better than the default parameters but the docked
conformations are still not optimal.
So are there any other parameters I should change to help access as much
of the conformational space as possible ? or should I try to increase the
parameters (ga_pop_size & ga_num_evals) I have already tried ? It is
already taking 24 hours to generate 10 conformations of my MacOSX G5, I
will try upping this to 100 as per the above paper but I won't see those
results for another 10 days or so. Any hints/suggestions appreciated.
Jeff Dyason e-mail:
J.Dyason at griffith.edu.au
Institute for Glycomics http://www.griffith.edu.au/glycomics
Griffith University (Gold Coast Campus)
PMB 50 Gold Coast Mail Centre Tel: +61 7 5552 7028
Queensland 9726 Australia Fax: +61 7 5552 8098
More information about the autodock