CAFASP, or the Critical Assessment of Fully Automated Structure Prediction, is a large-scale blind experiment in

protein structure prediction Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different ...

that studies the performance of automated structure prediction webservers in

homology modeling Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous pr ...

, fold recognition, and ''ab initio'' prediction of protein

tertiary structure Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may int ...

s based only on

amino acid sequence Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthes ...

. The experiment runs once every two years in parallel with

CASP Critical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. CASP prov ...

, which focuses on predictions that incorporate human intervention and expertise. Compared to related benchmarking techniques

LiveBench LiveBench is a continuously running benchmark project for assessing the quality of protein structure prediction and secondary structure prediction methods. LiveBench focuses mainly on homology modeling and protein threading but also includes secon ...

and

EVA Eva or EVA may refer to: * Eva (name), a feminine given name Arts, entertainment, and media Fictional characters * Eva (Dynamite Entertainment), a comic book character by Dynamite Entertainment * Eva (''Devil May Cry''), Dante's mother in t ...

, which run weekly against newly solved protein structures deposited in the

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...

, CAFASP generates much less data, but has the advantage of producing predictions that are directly comparable to those produced by human prediction experts. Recently CAFASP has been run essentially integrated into the CASP results rather than as a separate experiment.

References

External links

Protein Structure Prediction Center

CAFASP4 (2004)

CAFASP5 (2006)
Bioinformatics Protein methods {{bioinformatics-stub