Docking rigid-body

Reference Sampling Method Scoring Method DOF Resolution Runtime 7 

Gabdoulline and Wade46 BD Excluded volume and effective charge PB ES 6 Atomic lOh 

Meyer et al.49 Complete enumeration (FFT) Hydrogen-bond filtering and shape matching 6 ca. 1.5 A lh 

Ritchie and Kemp51 Complete enumeration (polynomial expansion) Electrostatic and shape matching 6 Depends on degree of polynomial used ih 

Hendrix and Kuntz53 Geometric hashing/ site-point matching + EM Shape matching + MM 6 ca. 1 A ih 

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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. 

Low-resolution rigid-body docking can be applied to a wide range of protein-protein complexes. These must display low-resolution recognition, a property found by Vakser et al.60 to be present in more than half of the complexes in a set of ca. 500 nonredundant protein-protein complex crystal structures. 

Two further energy functions based on Poisson-Boltzmann electrostatics and atomic solvation parameter (ASP)-based parameterizations of the solvation free energy changes43 were evaluated by Weng et al.57 in the context of side-chain optimization after rigid-body docking. 

Figure 7 The 20 highest ranking putative complexes from the best 100 FTDOCK candidates obtained after fine-grained rigid-body docking of the unbound barnase and barstar structures. Barnase is shown in the middle by dashed lines, surrounded by putative clusters of barstar orientations. The dense cluster to the right contains the correct docking orientation (shown in bold).

Another method of systematic search is the use of databases of pregenerated conformations. Conformations are calculated once and the search problem is reduced to a rigid body docking procedure. This is the main concept of FLOG docking program. ... 

Rigid body docking by Fourier correlation theory 366... 

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