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. Author manuscript; available in PMC: 2010 Apr 1.
Published in final edited form as: Curr Opin Struct Biol. 2009 Mar 25;19(2):164–170. doi: 10.1016/j.sbi.2009.02.008

TABLE 2.

Classification of docking methods based on the level of a priori information

Method Properties
 Examples
Search Examples
Global methods based
on Fast Fourier transform
(FFT) or geometric
hashing		 Global
systematic search		 Minimal;
smooth potential		 ZDOCK [7],
PIPER [20]
PatchDock [12]
MolFit [14]
Medium range methods
based on Monte Carlo
minimization		 Limited region,
stochastic search		 Moderate, mostly
side chains, some
loops		 RosettaDock [23]
ICM-DISCO [22]
Restraint-based
docking		 Specified by a priori
information on interface
residues		 Can be substantial HADDOCK [25]