EVA was a continuously running benchmark 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 differen ...

and secondary structure prediction methods. Methods for predicting both

secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...

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 p ...

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 differs ...

, and contact order prediction - were compared to results from each week's newly solved

protein structure Protein structure is the molecular geometry, 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 ami ...

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, c ...

. 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, in ...

s; this is similar to the related LiveBench project and stands in contrast to the bi-yearly benchmark CASP, 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