Re: CCL:AUTODOCK 3.0

["Garrett M. Morris" <garrett ( ( at ) ) scripps.edu>]

 Dear Simon,
 On Fri, 2 Jun 2000, Simon Cross wrote:
 > Has anyone used soft potentials with Autodock 3.0, or used other
 AutoGrid 3.1 has not yet been released, but it has a new form of
 pairwise potential smoothing, which ramps the potential to a finite
 value at separation zero.  This finite value can be varied by the
 user, and so could help dramatically in the early stages of the
 docking.
 > methods to overcome problems with 'gating' in a fixed receptor? I
 > am specifically working on antibodies and find that Autodock can
 > only reproduce the ligand location in the crystal structure if it
 > is initiated within the binding pocket - if the ligand is placed
 Are you using SA (simulated annealing) to do this?  You can only start
 the ligand at a pre-defined position using SA and LS (Solis and Wets).
 The GA and LGA start from a population of random initial genomes.
 > outside the binding pocket it docks in the correct location but
 > only 'half in' the pocket, presumably due to the lack of
 > flexibility of the antibody in this system.
 The LGA is the most efficient search method: SA seems to be the least
 efficient.  You should get better results with the LGA than with the
 SA, for the same number of energy evaluations. We found this even
 though both were started from random initial states or populations of
 states.
 If you are using LGA, with a population size of 50, an elitism number
 of 1, and a crossover rate of 0.80, you might want to try increasing
 elitism to 5.  Then there is a 20% chance that one of the top five do
 not experience crossover, and thus will survive into the next
 generation.
 Another pointer: increase the maxium number of evaluations, by a
 factor of 10.  This might help to improve the search results.
 > I am trying to get around this by using soft potentials but am not
 > entirely sure how to do this. Any comments much appreciated.
 >
 > -----------------------------------------
 >
 > Simon Cross
 > School of Chemistry
 > University of Nottingham
 > tel. 0115 9514193
 > Email: pcxsc ( ( at ) ) nottingham.ac.uk
 >
 >
 >
 >
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 I hope this helps,
 Garrett
 ___
 Dr Garrett M. Morris, MA, DPhil
 The Scripps Research Institute,       tel: (858) 784-2292
 Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
 10550  North Torrey Pines Road,       email: garrett ( ( at ) ) scripps.edu
 La Jolla,  CA 92037-1000,  USA.       www.scripps.edu/pub/olson-web/gmm