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Docking


\begin{problem}{Docking problem}\\
{\bf Input:} A receptor organic molecule $R...
...ligand surface
maximizing the contact area between the surfaces.
\end{problem}
There are several reasons for our interest in docking problems:

The main idea of docking is the "key in lock". The ligand is a key - small and sometimes flexible. The receptor is the lock, big and usually with a low level of flexibility. The better these two molecules fit - the better the influence of the drug and the interaction between them, will be. Researches have shown that there are molecules that are not completely rigid, but have partial flexibility. Usually the flexibility is in some spots, called hinges, between two parts of the molecule. In the hinges there is usually a determined range of angles where the rigid parts can rotate (see figure 13.19).


  
Figure 13.19: A molecule (two rigid parts and one hinge) and a receptor
\includegraphics{lec13_figs/Mol-Receptor.ps}

The class of docking problems has two major subclasses.

When evaluating docking methods, one should examine the following issues:

On figure 13.20 you can see a sketch of the different stages a docking method has.
  
Figure 13.20: Rigid and Flexible Docking.
\resizebox{7in}{!}{\includegraphics{lec13_figs/docking.eps}}


next up previous
Next: Bibliography Up: No Title Previous: Molecular Surface Representation
Peer Itsik
2001-03-04