CASP: An International Protein Structure Experiment

Deriving protein structures from genomic sequence data is the major challenge of contemporary computational biology. Genes are the blueprints for proteins, and the next step in harnessing the flood of data from genome research is using it to deduce the 3-D structure of proteins. For practical purposes, these problems are insoluble without advanced software and powerful computers.

Among research groups worldwide, many methods have arisen. CASP (Critical Assessment of Techniques for Protein Structure Prediction) is a community-wide experiment held every two years to assess these various computational approaches. "Through CASP," says PSC biochemist David Deerfield, "the field moves toward consensus on such questions as which methods are most accurate, which most cost-effective, where can future effort most effectively be directed?"

This year PSC and the Hewlett-Packard Company teamed to provide large-scale computational resources for CASP5, the fifth convening of this every-other-year event, for which participation has steadily grown to nearly 200 research groups worldwide. HP provided computing time on a 100-processor cluster of AlphaServer systems, and PSC made time available on LeMieux, PSC's terascale AlphaServer-based system.

A protein model

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