CAFASP
Encyclopedia
CAFASP, or the Critical Assessment of Fully Automated Structure Prediction, is a large-scale blind experiment in protein structure prediction
that studies the performance of automated structure prediction webservers in homology modeling
, fold recognition, and ab initio prediction of protein tertiary structure
s based only on amino acid sequence. The experiment runs once every two years in parallel with CASP
, which focuses on predictions that incorporate human intervention and expertise. Compared to related benchmarking techniques LiveBench
and EVA
, which run weekly against newly solved protein structures deposited in the Protein Data Bank
, 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.
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
that studies the performance of automated structure prediction webservers in homology modeling
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 protein...
, fold recognition, and ab initio prediction of protein tertiary structure
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
s based only on amino acid sequence. The experiment runs once every two years in parallel with CASP
CASP
CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994...
, which focuses on predictions that incorporate human intervention and expertise. Compared to related benchmarking techniques LiveBench
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 secondary structure prediction, comparing publicly...
and EVA
EVA (benchmark)
EVA is a continuously running benchmark project for assessing the quality of protein structure prediction and secondary structure prediction methods...
, which run weekly against newly solved protein structures deposited in the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
, 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.