Placing Fragments and Rigid Molecules

Since its first introduction in 1982, the DOCK software has been extended in several directions. The matching spheres can be labeled with chemical properties,61 and distance bins are used to speed up the search process.62,63 Recently, the search algorithm for distance-compatible matches was changed28 to the clique-detection algorithm introduced by Crippen and co-workers.55 Furthermore, several scoring functions are now applied in combination with the DOCK algorithm.64-68 

Several other approaches such as LUDI,69,70 CLIX,71 and ADAM72 are based on this clique-search paradigm although somehow differing in the features used for matching and in the way they are represented. 

Geometric hashing73 originated from the area of computer vision and was first applied to molecular docking problems by Fischer et al.74,75 In computer vision, the geometric hashing scheme was developed for the problem of recognizing (partially occluded) objects in camera scenes. In principle, 

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