Good binding site: Difference between revisions
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* sites on the interface of two domains, or at a flexible hinge region, can be problematic | * sites on the interface of two domains, or at a flexible hinge region, can be problematic | ||
[[Category:Preliminaries]] | |||
[[Category:DOCK Blaster]] |
Revision as of 21:53, 8 November 2007
There is a whole literature on the druggability of binding sites. Different people mean different things when they say "druggable". Here we discuss what makes a good binding site for docking small molecules, and thus, by extension, in our view, a site for which one can hope to find a low micromolar or better ligand
- site is deeply invaginated. Should hold a napthelene equivalent amount of ligand mass away from solvent
- protein-protein binding sites are a problem - they often are not deeply invaginated enough for tight small molecule docking
- sites with highly flexible loops, termini can be problems
- sites on the interface of two domains, or at a flexible hinge region, can be problematic