EVA: evaluation of protein structure prediction servers

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.

Simple fold composition and modular architecture of the nuclear pore complex

“…The agreement is as high as 87% of the residues for some of the models, when a three-state assignment (helix, strand, and other) is used. This agreement is the maximum possible level of consistency given the Ϸ75% accuracy of the secondary structure prediction methods (22). Fifth, protease accessibility laddering corroborates our fold assignments ( Fig.…”

A Comprehensive Structure-Based Alignment of Prokaryotic and Eukaryotic Neurotransmitter/Na+Symporters (NSS) Aids in the Use of the LeuT Structure to Probe NSS Structure and Function

“…The results from several of the best-performing secondary structure prediction methods (Koh et al, 2003) [i.e., PROFphd (Rost et al, 2004), Sspro (Pollastri et al, 2002), and PSIPRED (Jones, 1999)] were used to guide the alignment of the second and fourth extracellular loops (EL2 and EL4).…”

The AidB Component of the Escherichia coli Adaptive Response to Alkylating Agents Is a Flavin-Containing, DNA-Binding Protein

“…The 34 nonredundant, full-length AidB-like sequences were aligned (Fig. S2 in the supplemental material) using the TCoffee webserver (http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee _cgi/index.cgi), which is the best-validated multiple sequence alignment method (19). Despite the evolutionary distance between the organisms, AidB is highly conserved, with no less than 67 absolutely conserved residues (numbering is based on the E. coli AidB sequence): Asn10, Ala62, Pro67, Gly76, Arg78, Pro86, Cys133, Pro134, Met137, Thr138, Lys175, Gly181, Thr185, Glu186, Lys187, Gln188, Gly189, Gly190, Asp192, Ala200, Gly212, His213, Lys214, Phe216, Ser218, Pro220, Asp223, Cys237, Phe238, Pro241, Asn250, Leu257, Lys258, Lys260, Gly262, Asn263, Asn266, Ser268, Glu270, Glu272, Gly282, Gly287, Met294, Thr298, Arg299, Arg311, Arg324, Leu331, Met337, Arg375, Lys382, Glu395, Glu398, Gly401, Gly402, Gly404, Arg413, Glu417, Pro419, Trp424, Glu425, Gly426, Gly428, Asn429, Asp434, Arg437, and Arg483.…”