Rigid-body docking algorithms

In principle, every conformer of a set of flexible ligands could be stored in a database, and then each conformation could be evaluated with rigid-body docking algorithms. The size of the ensemble is critical since the computing time increases linearly with the number of conformations and the quality of the result drops with larger differences between the most similar conformation of the ensemble and the actual complex conformation. Thus a balance must be struck between computing time requirements and the desire to cover all of conformational space. 

The major limitation of the rigid-body docking algorithms is that the conformational flexibility of the ligand molecule is not considered. Often small molecules have large conformational spaces with several low energy states. Even for small molecules with only a few rotatable bonds significant differ-... 

In each of the introduced algorithms for rigid-body docking, the superposition of point sets is a fundamental subproblem that has to be solved efficiently and therefore is discussed here shortly ... 

In the following two sections, we report current methods for rigid- and flexible-body docking. After describing the algorithmic ideas, we make a rough classification and highlight the limits and capabilities of the respective methods. 

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