Docking flexible protein handling

Flexible Protein Handling in Protein-Ligand Docking 225... 

Flexible Protein Handling in Docking-Based Virtual Screening... 

The docking problem in its full generality is likely to remain an open problem even in the long term. Too many subproblems are still unsolved, the most urgent ones being the accurate prediction of binding affinity and the handling of protein conformational flexibility. 

Protein flexibility as the second major challenge is discussed in two separate chapters. The first is dedicated primarily to the algorithmic description of the methods available for handling protein flexibility, based on a new classification of the different approaches. The second chapter focuses on their application in high-throughput docking and virtual screening. As these chapters illustrate, a multitude of different approaches are already available for at least partial consideration of protein... 

An additional problem with crystal structures that can give rise to a misleading model is the thermal motion and disorder within the crystalline lattice. Local regions of electron density can be poorly defined, even for structures with relatively good resolution if, for example, a protein residue is labile in the crystalline state. If undetected, a residue can be poorly modeled, misassigned, or omitted from the model. Even when detected and fully modeled, disorder implies flexibility, which may need specific handling in a docking study. 

Ichinose, T, Nakamura, K and Itai, A. (2006) Effective handling of induced-fit motion in flexible docking. Proteins,... 

Handling Protein Flexibility in Docking and High-Throughput Docking From Algorithms to Applications... 

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