Failures Due to Protein Flexibility

The impact of receptor flexibility on docking is usually assessed by cross-docking experiments, whereby a series of ligands is docked to all their corresponding 

PD1663 26 (light gray carbon atoms) binds to position (PDB lOPK, light blue ribbon). Color the receptor with the activation loop (brown) in code for noncarbon atoms oxygen, red  

However, larger compound imatinib (dark gray with pyMol (www.pymol.org). 

Accounting for Protein Flexibility in Docking-Based Drug Discovery and Design 

3) Multilevel methods, where protein flexibility is accounted for at least in two independent stages of the docking protocol. This is the case of the relaxed complex scheme (RCS) [52, 53], in which an ensemble of unbound target structures is generated by MD and then used to dock a small chemical library 

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