Use of Protein-Based Constraints in Docking

Many techniques for constraining docking have been developed for different docking programs different docking programs will use different strategies to implement the constraints provided. 

Use of constraints is to be encouraged in virtual screening when the condition implied by the constraint is a known precondition for binding, but a user should consider that by constraining dockings one may preclude possible unknown modes of binding. 

This simple example illustrates that the selection of the protein structure and also the explicit or implicit treatment of protein flexibility can have a large impact on docking results. Selecting a single receptor structure based on the assumption that all ligands bind to the same protein conformation can be misleading as observed for protein structure IqSu. A priori it is usually unknown which single protein structure 

Correctly predicted ligand conformations are colored green, v hile w rong ones are colored red. The optimum ranking is AAD. 

Protein structures are delightful to study, but equally enigmatic. This chapter highlights a number of specific features that need consideration when using protein structures in vHTS, but broadly these can be summarized into a small number of recommendations. These are as follows  

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