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Structural Bioinformatics, 2nd Edition by Philip E. Bourne, Jenny Gu

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28

CASP AND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION

Jenny Gu and Philip E. Bourne

A MEASURE FOR SUCCESS

In the early 1990s, the community recognized that methods for structure determination from sequence information have been proliferating, creating the need to benchmark these developments to gauge the utility of the algorithms to the biological community and to measure the progress in this developing field of structure prediction. In part, this need also came from users of these tools concerned by over optimistic claims of prediction performance. In 1994, John Moult pioneered the idea that the only way to objectively assess the utility of these tools was to conduct a blind experiment in which predictions were made on protein structures not yet publicly available, but with available sequences (Moult et al., 1995). critical assessment of structure prediction (CASP) was born and, through this assessment, confidence from the user community can be said to have been reclaimed. Even a prediction of limited accuracy can be useful if the user knows what to expect and the method has been cross-validated. The CASP experiment consists of three parts: defining the types of predictions to be performed (this has changed over time), the collection of prediction targets, and the evaluation of the performance of each predictor. For the first competition, the field was evaluated in three categories: comparative modeling, threading, and ab initio prediction. ...

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