EVA was a continuously running
benchmark
Benchmark may refer to:
Business and economics
* Benchmarking, evaluating performance within organizations
* Benchmark price
* Benchmark (crude oil), oil-specific practices
Science and technology
* Benchmark (surveying), a point of known elevati ...
project for assessing the quality and value of
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 ...
and
secondary structure prediction methods. Methods for predicting both
secondary structure
Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
and
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 ...
- including
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 ...
,
protein threading
Protein threading, also known as fold recognition, is a method of protein modeling which is used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure.
It differ ...
, and
contact order The contact order of a protein is a measure of the locality of the inter-amino acid contacts in the protein's native state tertiary structure. It is calculated as the average sequence distance between residues that form native contacts in the folde ...
prediction - were compared to results from each week's newly solved
protein structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer ma ...
s 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 ...
. The project aimed to determine the prediction accuracy that would be expected for non-expert users of common, publicly available prediction
webserver
A web server is computer software and underlying hardware that accepts requests via HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, commonly a web browser or web crawler, initiate ...
s; this is similar to the related
LiveBench project and stands in contrast to the bi-yearly benchmark
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 aims to identify the maximum accuracy achievable by prediction experts.
References
* Rost B, Eyrich VA. (2001). EVA: large-scale analysis of secondary structure prediction. ''Proteins'' Suppl 5:192-9.
* Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. (2001). EVA: continuous automatic evaluation of protein structure prediction servers. ''Bioinformatics'' 17(12):1242-3.
* Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Grana O, Pazos F, Valencia A, Sali A, Rost B. (2003). EVA: Evaluation of protein structure prediction servers. ''Nucleic Acids Res'' 31(13):3311-5.
External links
EVA main site
{{bioinformatics-stub
Bioinformatics
Protein methods