Structure based ligand discovery: Difference between revisions
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Structure based ligand discovery is the use of | Structure based ligand discovery is the use of | ||
a macromolecular (usually protein) structure to discover new | a macromolecular (usually protein) structure to discover new ligands. At a high level, there are three ways to go about this: | ||
1. have an expert look at the model, and draw a molecule that complements the binding site. | 1. have an expert look at the model, and draw a molecule that complements the binding site. | ||
2. Perform #1 using an automatic program. This is called [[ | 2. Perform #1 using an automatic program. This is called [[de novo design]]. | ||
3. Dock a database of small molecules into the binding site, and rank them from best to worst. | 3. Dock a database of small molecules into the binding site, and rank them from best to worst. | ||
Revision as of 01:15, 12 February 2009
Structure based ligand discovery is the use of a macromolecular (usually protein) structure to discover new ligands. At a high level, there are three ways to go about this:
1. have an expert look at the model, and draw a molecule that complements the binding site. 2. Perform #1 using an automatic program. This is called de novo design. 3. Dock a database of small molecules into the binding site, and rank them from best to worst.
The problem with method #1 is that it is very labor intensive, and that any compound invented may be difficult and/or expensive to make. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitations. It can also be, relatively speaking, slow.
The third approach, docking, is the one taken by DOCK and its graphical user interface, DOCK Blaster.