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Mapping the protein world

RP/wARP was the first, and for a while the only, software that could generate models to fit experimental data automatically and very accurately. It has cut down the time necessary to create structural models from weeks to minutes.

This grant will allow the scientists to explore new concepts of model-building and enlarge the scope of data that the software can handle. ARP/wARP deals very well with high-resolution data that allows to distinguish individual atoms, but much of the data that scientists have to deal with is of lower quality. The software has steadily been improved to work with lower-resolution data, and Lamzin and Perrakis know how to stretch it even further.

"The high-throughput revolution in Structural Biology allows us to work on more and more complex problems relevant to human health," Perrakis says. "Knowing the structures of molecules that play crucial roles in cancer, cardiovascular and neurodegenerative diseases and molecules from pathogenic bacteria or viruses will contribute to design new revolutionary therapeutic strategies."

To meet this objective the scientists intend to study crystals of proteins bound to diverse drug candidates or containing different types of large molecules.

"ARP/wARP needs to meet a two fold challenge: firstly, it needs to be able to work with structural information at lower resolution, within the range of 3.0 to 3.5 Ångstroms, and secondly, the models produced have to be complete and validated. The new NIH grant will help us to approach these aims. In the future researchers will be able to focus on structure analysis rather than just building the structure and, who knows, by combining ARP/wARP with new cell imaging techniques we might be able to model the molecules of a complete cell," Perrakis concludes.


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Source:European Molecular Biology Laboratory


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