Powerful online tool for protein analysis provided pro bono by Stanford ...( STANFORD Calif. Scientists around th...)

STANFORD, Calif. Scientists around the world may benefit from a powerful new database, available for free online, that will help them to home in on the parts of proteins most necessary for their function.

Arend Sidow, PhD, associate professor of pathology and of genetics at the Stanford University School of Medicine, recently launched the novel bioinformatics tool, which enlists evolution as the guide to determining the role different proteins play in a wide array of organisms.

ProPhylER (http://www.prophyler.org), which Sidow has been working on since 2002, will enable a researcher studying a protein, or the gene coding for it, to more easily figure out how it works and whether something might go wrong if the gene has a mutation. "Whether you're a cell biologist, biochemist or structural biologist, ProPhylER produces instant working hypotheses for you as to where the protein's functional areas are," he said. The site made its debut on Oct. 10.

Proteins the machines of life that do everything from making your muscles move to helping you breathe and think are long chains of small chemical units called amino acids. As soon as a protein molecule is made inside a cell from the gene encoding it, it folds up to assume the unique shape that determines its activity. To do its job, a protein needs to have specific amino acids (there are 20 to pick from) in specific places. In particular regions of the folded protein, it may be crucial that a specific amino acid sequence be there in order for the protein to function; in other regions, the swapping of one amino acid for another has little effect.

Over the course of several hundreds of millions of years myriad species have evolved, and, through eons of random mutation, so have their proteins. Yet in the face of all these changes, some things have to remain constant. "Evolution imposes stronger constraints on more-important regions of a protein mol
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