Abstract A new optimization model of molecular docking
is proposed, and a fast flexible docking method based on an
improved adaptive genetic algorithm is developed in this
paper.The algorithmtakes some advanced techniques, such as
multi-population genetic strategy, entropy-based searching
technique with self-adaptation and the quasi-exact penalty. A
new iteration scheme in conjunction with above techniques is
employed to speed up the optimization process and to ensure
very rapid and steady convergence. The docking accuracy and
efficiency of the method are evaluated by docking results from
GOLD test data set, which contains 134 protein–ligand
complexes. In over 66.2% of the complexes, the docked pose
was within 2.0 A ° root-mean-square deviation (RMSD) of the
X-ray structure. Docking time is approximately in proportion
to the number of the rotatable bonds of ligands.