Science Buddies: "Ask an Expert"

Would it be possible to design an algorithm that seperates and classifies outer membrane proteins in gram-negative bacteria based on frequently occuring subsequences of amino acids? Aren't outer membrane proteins usually investigated as targets for drugs? Perhaps I've just made myself sound extremely ignorant, but if there's any possibility of such a project, I'd like to pursue it. Thanks in advance for any information.

-Bill

Bill,

I am not quite clear what you mean by "separates and classifies outer membrane proteins." What exactly do you want your algorithm to do? Are you interested in integral or peripheral proteins? Are you trying to separate membrane proteins from other structural proteins? If you can be a bit more specific, I can help you determine the feasablility of your idea.

FYI: Most drug research focuses on interrupting one or more of the steps of protein production in the cell. Some drugs block signal transduction pathways, others act as competitive or nonceompetitive inhibitors to enzyme function, and others interfere with protein synthesis itself.

It would be helpful if I knew the amount of biology background that you have.