Can anyone suggest which software or strategy is appropriate to find how binds small molecule to protein? for example some inhibitor that prohibits aggregation of some protein, how to predict where it binds?
Another question is how to study the binding in vitro? and design experiment?
Try going through the following articles and see if they help.
http://nar.oxfordjournals.org/content/early/2011/05/14/nar.gkr356.short
http://cpclab.uni-duesseldorf.de/publications/publications/13.pdf
Docking programmes are very useful to detect the inhibition potential of a ligand (small molecule) against bulky molecule (protein). They can tell about the specific area and type of bonds could make and it's stability. These results usually similar to the in vitro studies. Auto dock docking programme is available and free to use. With expert advices and few practices valuable information can be gained.
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