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Mapping the protein world

In the early days of X-ray crystallography obtaining a three-dimensional model of a protein required wire models, screws, bolts and years of tedious calculations by hand. Today macromolecular models are built by computers ?thanks to sophisticated software and in particular a package called ARP/wARP. Developed by Victor Lamzin at the Hamburg Outstation of the European Molecular Biology Laboratory (EMBL) and Anastassis Perrakis at the Netherlands Cancer Institute (NKI) in Amsterdam, ARP/wARP is currently used by over 2,000 researchers throughout the world. The capabilities of this software will now expand even further - thanks to a grant of over 800,000 US Dollars from the U.S. National Institutes of Health (NIH).

The grant, which will run over four years, comes at a perfect time. "More than 1,000 research laboratories from over 50 countries are holding ARP/wARP licenses and by June this year our paper that described the key innovative feature of ARP/wARP in Nature Structural Biology in 1999 has reached the magic number of 1,000 citations in the scientific literature. This has created an incredible drive for further scientific development," Lamzin says. "The new funding gives us a push to advance the software's ability to recognise and distinguish different types of macromolecular objects, for example DNA, and to improve the automated generation of structural models. ARP/wARP has made the life of structural biologists worldwide a lot easier and will do even more so once the new features planned under the NIH grant have been implemented."

ARP/wARP transforms 'electron density maps', produced in experiments that bombard protein crystals with X-rays, into 3-dimensional structures. "X-ray experiments result in 'diffraction patterns' that can't be interpreted using our eyes," Lamzin says. "These have to be reconstructed into a three-dimensional image through mathematics and models. This was a very tedious, time-consuming, and subjective process."

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Source:European Molecular Biology Laboratory


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