Overview of a typical docking procedure. This diagram summarizes the consensus approach based on rigid body docking followed by re-ranking and refinement. Approaches vary according to whether the steps are combined or performed independently in a particular program. Many strategies only perform some stages, particularly the initial docking and scoring or just subsequent re-ranking and refinement. Biological distance constraints can be included at different stages in the procedure.
practice, the current status of the algorithms is that they generate a limited list of possible complexes ranked on the score and the objective is that one member of the list should be close to the true complex.
vi. At this stage, a re-ranking of the resultant complexes can be undertaken possibly using computationally more intensive calculations.
vii. Conformational flexibility is generally introduced into the algorithm when there is only a limited number of complexes to consider. Perturbations to the structure of the docked complex are made and the energies of the resultant conformation is evaluated. The aims are both to improve the structural quality of the predicted complex and to improve the power of identifying the true solution from the set of false structures that have been generated.
A summary of the current status of protein-protein docking is that when this strategy has been applied to around ten test systems, one can generate a close model (2.5 A rmsd for the Ca atoms) to the true complex at a rank of ten or less for many of the systems studied.
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