SOFTWARE: Molecules on Parade

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Science  25 Jul 2003:
Vol. 301, Issue 5632, pp. 443
DOI: 10.1126/science.301.5632.443b

Aimed at everyone from drug designers to researchers tracking the nuances of protein evolution, Chimera is a jazzy molecular modeling package from the Computer Graphics Lab at the University of California, San Francisco. Users can import atomic coordinates from databases such as the Protein Data Bank or upload their own measurements, then manipulate and analyze molecular architecture. The program flags likely hydrogen bonds and pinpoints landmarks such as helices or sheets within messy 3D data. You can create catchy graphics—for example, the program lets you install windows in bulky molecules to expose their internal organization. What looks like a piece of chewed bubblegum in this image is a molecule of the antitumor drug netropsin wedged between two DNA strands. Chimera can also parse protein sequence data, aligning matching segments and illustrating the structures they encode. The package is free for researchers in academia, government, and nonprofit organizations, and its creators plan to release a revamped version every 6 months.

www.cgl.ucsf.edu/chimera

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