Protein Structure and Function. Application of Bioinformatics Methods - John Rigden 2014

Fold recognition
Introduction
The importance of "blind" tests: The CASP competition

Over the past 30 years, a vast array of Methods has been developed aimed at solving Structure/149.html">The problem of Cell/13.html">Protein Structure Prediction in general and identifying folding patterns in particular. As with other scientific endeavors, it is critically important in this case that any new technique be thoroughly tested "experimentally." This is precisely why the Critical Assessment of Structure Prediction (CASP) competition was established (http://predictioncenter.llnl.gov/; Moult et al. 2007). The goal of the CASP competition, or workshop (held biennially), is to model the Native State of an Amino Acid Sequence whose structure is unknown. However, there is an important caveat: the organizers of the competition do know the structure. The structures of the Proteins proposed for consideration in the competition are determined by experimental methods shortly before the event, but these data are withheld from the scientific community until the competition concludes. As a result, the competition assessors are in a rather unique situation: they know the Spatial Structure of A number of proteins that remain entirely unknown to the predictors.

CASP Functions as a "blind" experimental evaluation system for various structure prediction methods under real-world conditions; therefore, the very idea of the CASP competitions was used to determine the set of methods described in this chapter. This does not imply at all that methods not covered here fail to yield reliable results that simply were not showcased in CASP for some reason. Literally hundreds of structure prediction methods have been developed in recent years, and to avoid overwhelming the reader, the results of the CASP competitions are used as a filter. An Overview of the latest CASP7 results is provided in the supplementary Materials for CASP7 (Moult et al. 2007).

2 Recall that as of early 2013, the number of structures in the PDB database is approximately 87,000. Translator's Note.



Last update: 06/08/2026

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