SOFTWARE: Bent Into Shape

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Science  16 May 2003:
Vol. 300, Issue 5622, pp. 1061
DOI: 10.1126/science.300.5622.1061c

When an antibody sticks to a viral protein, marking it for annihilation by certain immune cells, the two molecules don't just snap into place like puzzle pieces. Instead, the antibody must bend or twist in order to get a grip. The program AutoDock predicts the structural contortions that molecules undergo when they couple with proteins or DNA. Academic scientists can obtain AutoDock for free through this site created by computational chemist Garrett Morris of the Scripps Research Institute in La Jolla, California. The results are useful for deciphering chemical mechanisms, designing drugs, and other applications in which scientists need to know the shape of interacting molecules, Morris says. For example, AIDS researchers can screen potential antiviral compounds by determining which ones will cozy up to HIV proteins.

Shape-shifting molecules also star at the Database of Simulated Molecular Motions from the European Media Laboratory in Heidelberg, Germany. The site allows you to screen more than 100 computer simulations (some housed on other sites) of molecules folding, unfolding, jiggling, docking, or slicing apart other molecules. For example, you can tour the sodium-potassium pump, which ushers ions through the cell membrane, or watch the estrogen receptor grab a length of DNA. Scientists are invited to contribute their own flicks to the site.

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