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docking and minimization

Pedro M Coutinho pedro at iastate.edu
Thu Sep 22 17:40:32 EST 1994



>Dear xtallographers and modellers-
>	I wanted to dock two proteins
>together and then minimize to get some
>numbers for goodness-of-fit but can't
>afford insight or other megabuck programs.
>is there shareware/econoware for this task.

A reference that might be useful is:

Stoddard, B.L. & Koshland, D.E. (1992) "Prediction of a receptor protein
complex using a binary docking method." Nature. 358 (6389): 774-776

A version of the docking software AutoDock to make this study.  
Information on licensing (free for academics) is available from Peggy 
Graber at The Scripps Research Institute: graber at scripps.edu 

The only problem of the approach is that the input files still require
processing by Biosym Insight (Discover) or Sybil but the quality of the
results seems to be very good.

I hope this helps! 


--------------------------------- H2N-CH-CO-NH-CH-CO-...-NH-CH-COOH --
Pedro M. Coutinho  - Graduate Student  \        \            \
IOWA STATE UNIVERSITY                   R1       R2           Rn
Department of Chemical Engineering               Phone: 1-515-294-9370
2114 Sweeney Hall                                Fax:   1-515-294-2689  
Ames, IA 50011-2230                          E-mail: pedro at iastate.edu
U.S.A.                      URL: http://www.public.iastate.edu/~pedro/

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