Literature DB >> 11751240

EVA: continuous automatic evaluation of protein structure prediction servers.

V A Eyrich1, M A Martí-Renom, D Przybylski, M S Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali, B Rost.   

Abstract

UNLABELLED: Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu

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Year:  2001        PMID: 11751240     DOI: 10.1093/bioinformatics/17.12.1242

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  49 in total

1.  MODBASE, a database of annotated comparative protein structure models.

Authors:  Ursula Pieper; Narayanan Eswar; Ashley C Stuart; Valentin A Ilyin; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  Comparing function and structure between entire proteomes.

Authors:  J Liu; B Rost
Journal:  Protein Sci       Date:  2001-10       Impact factor: 6.725

3.  The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.

Authors:  Jürgen Kopp; Torsten Schwede
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  MODBASE, a database of annotated comparative protein structure models, and associated resources.

Authors:  Ursula Pieper; Narayanan Eswar; Hannes Braberg; M S Madhusudhan; Fred P Davis; Ashley C Stuart; Nebojsa Mirkovic; Andrea Rossi; Marc A Marti-Renom; Andras Fiser; Ben Webb; Daniel Greenblatt; Conrad C Huang; Thomas E Ferrin; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  Accurate and automated classification of protein secondary structure with PsiCSI.

Authors:  Ling-Hong Hung; Ram Samudrala
Journal:  Protein Sci       Date:  2003-02       Impact factor: 6.725

6.  Transmembrane helix predictions revisited.

Authors:  Chien Peter Chen; Andrew Kernytsky; Burkhard Rost
Journal:  Protein Sci       Date:  2002-12       Impact factor: 6.725

7.  Static benchmarking of membrane helix predictions.

Authors:  Andrew Kernytsky; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

8.  META-PP: single interface to crucial prediction servers.

Authors:  Volker A Eyrich; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

9.  Tools for comparative protein structure modeling and analysis.

Authors:  Narayanan Eswar; Bino John; Nebojsa Mirkovic; Andras Fiser; Valentin A Ilyin; Ursula Pieper; Ashley C Stuart; Marc A Marti-Renom; M S Madhusudhan; Bozidar Yerkovich; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

10.  Learning biophysically-motivated parameters for alpha helix prediction.

Authors:  Blaise Gassend; Charles W O'Donnell; William Thies; Andrew Lee; Marten van Dijk; Srinivas Devadas
Journal:  BMC Bioinformatics       Date:  2007-05-24       Impact factor: 3.169

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