Anchor docking

Fig. 10.4. (a) Crystal structure of gp11 p-HSD1 complex with Reactant A which was used as defining ligand in docking simulations, (b) Adamantyl amide core structure used in fixed anchor docking. 

Fixed anchor docking allows the docking of one part of a ligand while keeping the portion of the ligand that is primarily... 

Fig. 10.13. Examples of dock poses from fixed anchor docking of the virtual library in gp11 p-HSDI crystal structure.

Structure file (in SDF format) of the virtual library compounds to be subjected to fixed anchor or partially fixed docking... 

In neurons, the SNARE complex consists of three main proteins the v-SNARE synaptobrevin or VAMP (vesicle-associated membrane protein), and two t-SNAREs, syntaxin and SNAP-25 (synaptosomal associated protein of 25 kD). Synaptobrevins traverse the synaptic vesicle membrane in an asymmetric manner a few amino acids are found inside the vesicle, but most of the molecule lies outside the vesicle, within the cytoplasm. Synaptobrevin makes contact with another protein anchored to the plasma membrane of the presynaptic neuron, syntaxin, which is associated with SNAP-25. Via these interactions, the SNARE proteins play a role in the docking and fusion of synaptic vesicles to the active zone. 

A structure-based example is to explore a given subsite in a protein active site. The special feature is positioned as a site point where the molecules to dock will be anchored this could be done using the position of the atom of the docked scaffold which is used to link the reagents or the derivative... 

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