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New approach builds better proteins inside a computer
Date:10/17/2007

the analysis, using a selection process inspired by natural evolution. Each iteration produces a set of structurally different models, from which those lowest in energy are chosen for the next round of computational rebuilding and refinement. Ultimately, the lowest energy model wins out.

Its as if you had many species of animals all competing with one another, said Baker. The idea is that you take the fittest from each population and let those compete, ultimately arriving at the fittest animal of all.

The paper represents a real breakthrough, wrote structural biologist Eleanor Dodson in a News & Views editorial also published online by Nature. Dodson writes, This approach demonstrates real progress in several respects: the use of enormous computational power; the exploitation of known three-dimensional structures; the development of powerful search algorithms that relate those structures to new sequences; and the steadily improving tactics used to determine low-energy conformations of molecules.

The benefits will be seen in structure-based drug design and in improved models for crystallographic calculations. And in the future, this method might provide structural information about intractable molecules that are difficult to study experimentally, wrote Dodson, who is at the University of York in the United Kingdom.

Baker and his colleagues demonstrated the value of their technique by using it to improve data on protein structures derived using both x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. NMR spectroscopy analyzes the magnetic properties of atomic nuclei in molecules to gain insight into their structure. While both techniques are highly useful in analyzing protein structure, the data they yield have ambiguities that predictive protein structure modeling can resolve, said Baker. Specifically, they noted that the new computational method alleviates the crystallographic phase problem for small proteins by generating high a
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Contact: Jim Keeley
keeleyj@hhmi.org
301-215-8858
Howard Hughes Medical Institute
Source:Eurekalert

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