EVA: Evaluation of protein structure prediction servers - PubMed (original) (raw)

EVA: Evaluation of protein structure prediction servers

Ingrid Y Y Koh et al. Nucleic Acids Res. 2003.

Abstract

EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods. The evaluation is updated automatically each week, to cope with the large number of existing prediction servers and the constant changes in the prediction methods. EVA currently assesses servers for secondary structure prediction, contact prediction, comparative protein structure modelling and threading/fold recognition. Every day, sequences of newly available protein structures in the Protein Data Bank (PDB) are sent to the servers and their predictions are collected. The predictions are then compared to the experimental structures once a week; the results are published on the EVA web pages. Over time, EVA has accumulated prediction results for a large number of proteins, ranging from hundreds to thousands, depending on the prediction method. This large sample assures that methods are compared reliably. As a result, EVA provides useful information to developers as well as users of prediction methods.

PubMed Disclaimer

Figures

Figure 1

Flowchart of EVA. Every day, EVA downloads the newest protein structures from PDB (4). The structures are added to mySQL databases, sequences are extracted for every protein chain and are sent to each prediction server by META-PredictProtein (5) (except for threading in which only novel structures are sent). META-PP collects the results and sends them to EVA. Every week, predictions of secondary structure, threading/fold recognition, comparative modelling and inter-residue contacts are evaluated at the EVA satellites at Columbia University, University of California, San Francisco, and CNB Madrid. The central EVA site at Columbia collects all the assessments from the satellites and the results from the database searches, and publishes the updated web pages. Finally, all web pages are mirrored at the satellites.

Cited by

Membrane protein prediction methods.
Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B. Punta M, et al. Methods. 2007 Apr;41(4):460-74. doi: 10.1016/j.ymeth.2006.07.026. Methods. 2007. PMID: 17367718 Free PMC article. Review.
Tools for comparative protein structure modeling and analysis.
Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Eswar N, et al. Nucleic Acids Res. 2003 Jul 1;31(13):3375-80. doi: 10.1093/nar/gkg543. Nucleic Acids Res. 2003. PMID: 12824331 Free PMC article.
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. Pieper U, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22. doi: 10.1093/nar/gkh095. Nucleic Acids Res. 2004. PMID: 14681398 Free PMC article.
A dynamic Bayesian network approach to protein secondary structure prediction.
Yao XQ, Zhu H, She ZS. Yao XQ, et al. BMC Bioinformatics. 2008 Jan 25;9:49. doi: 10.1186/1471-2105-9-49. BMC Bioinformatics. 2008. PMID: 18218144 Free PMC article.
Sequence-based prediction of protein domains.
Liu J, Rost B. Liu J, et al. Nucleic Acids Res. 2004 Jul 7;32(12):3522-30. doi: 10.1093/nar/gkh684. Print 2004. Nucleic Acids Res. 2004. PMID: 15240828 Free PMC article.

References

1. Eyrich V., Martí-Renom,M.A., Przybylski,D., Fiser,A., Pazos,F., Valencia,A., Sali,A. and Rost,B. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242–1243. - PubMed
1. Rost B. and Eyrich,V. (2001) EVA: large-scale analysis of secondary structure prediction. Proteins, 45 (Suppl. 5), S192–S199. - PubMed
1. Marti-Renom M.A., Madhusudhan,M.S., Fiser,A., Rost,B. and Sali,A. (2002) Reliability of assessment of protein structure prediction methods. Structure, 10, 435–440. - PubMed
1. Berman H.M., Westbrook,J., Feng,Z., Gillliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235–242. - PMC - PubMed
1. Eyrich V.A. and Rost,B. (2003) META-PP: single interface to selected web servers. Nucleic Acids Res., 31, 3308–3310. - PMC - PubMed

EVA: Evaluation of protein structure prediction servers - PubMed (original) (raw)