Literature DB >> 15608124

LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction.

Leszek Rychlewski1, Daniel Fischer.   

Abstract

We present the results of the evaluation of the latest LiveBench-8 experiment. These results provide a snapshot view of the state of the art in automated protein structure prediction, just before the 2004 CAFASP-4/CASP-6 experiments begin. The last CAFASP/CASP experiments demonstrated that automated meta-predictors entail a significant advance in the field, already challenging most human expert predictors. LiveBench-8 corroborates the superior performance of meta-predictors, which are able to produce useful predictions for over one-half of the test targets. More importantly, LiveBench-8 identifies a handful of recently developed autonomous (nonmeta) servers that perform at the very top, suggesting that further progress in the individual methods has recently been obtained.

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Year:  2005        PMID: 15608124      PMCID: PMC2253323          DOI: 10.1110/ps.04888805

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  25 in total

1.  Comparison of sequence profiles. Strategies for structural predictions using sequence information.

Authors:  L Rychlewski; L Jaroszewski; W Li; A Godzik
Journal:  Protein Sci       Date:  2000-02       Impact factor: 6.725

2.  Enhanced genome annotation using structural profiles in the program 3D-PSSM.

Authors:  L A Kelley; R M MacCallum; M J Sternberg
Journal:  J Mol Biol       Date:  2000-06-02       Impact factor: 5.469

3.  MaxSub: an automated measure for the assessment of protein structure prediction quality.

Authors:  N Siew; A Elofsson; L Rychlewski; D Fischer
Journal:  Bioinformatics       Date:  2000-09       Impact factor: 6.937

4.  CASP5. Proceedings of the 5th Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. 1-5 December 2002, Asilomar, California, USA.

Authors: 
Journal:  Proteins       Date:  2003

5.  CAFASP3: the third critical assessment of fully automated structure prediction methods.

Authors:  Daniel Fischer; Leszek Rychlewski; Roland L Dunbrack; Angel R Ortiz; Arne Elofsson
Journal:  Proteins       Date:  2003

6.  The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries.

Authors:  Daniel Fischer; Jakub Paś; Leszek Rychlewski
Journal:  Bioinformatics       Date:  2004-04-08       Impact factor: 6.937

7.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

8.  Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium.

Authors:  D Fischer; D Eisenberg
Journal:  Proc Natl Acad Sci U S A       Date:  1997-10-28       Impact factor: 11.205

Review 9.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

10.  Dali: a network tool for protein structure comparison.

Authors:  L Holm; C Sander
Journal:  Trends Biochem Sci       Date:  1995-11       Impact factor: 13.807

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  33 in total

1.  Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p.

Authors:  Anna Czerwoniec; Janusz M Bujnicki
Journal:  Cell Cycle       Date:  2011-10-15       Impact factor: 4.534

2.  CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups.

Authors:  Boris Vishnepolsky; Malak Pirtskhalava
Journal:  Protein Sci       Date:  2011-11-23       Impact factor: 6.725

3.  All are not equal: a benchmark of different homology modeling programs.

Authors:  Björn Wallner; Arne Elofsson
Journal:  Protein Sci       Date:  2005-05       Impact factor: 6.725

4.  A composite score for predicting errors in protein structure models.

Authors:  David Eramian; Min-yi Shen; Damien Devos; Francisco Melo; Andrej Sali; Marc A Marti-Renom
Journal:  Protein Sci       Date:  2006-06-02       Impact factor: 6.725

Review 5.  Membrane protein prediction methods.

Authors:  Marco Punta; Lucy R Forrest; Henry Bigelow; Andrew Kernytsky; Jinfeng Liu; Burkhard Rost
Journal:  Methods       Date:  2007-04       Impact factor: 3.608

Review 6.  Progress and challenges in protein structure prediction.

Authors:  Yang Zhang
Journal:  Curr Opin Struct Biol       Date:  2008-04-22       Impact factor: 6.809

7.  BCL::contact-low confidence fold recognition hits boost protein contact prediction and de novo structure determination.

Authors:  Mert Karakaş; Nils Woetzel; Jens Meiler
Journal:  J Comput Biol       Date:  2010-02       Impact factor: 1.479

8.  Island method for estimating the statistical significance of profile-profile alignment scores.

Authors:  Aleksandar Poleksic
Journal:  BMC Bioinformatics       Date:  2009-04-20       Impact factor: 3.169

9.  TIM-Finder: a new method for identifying TIM-barrel proteins.

Authors:  Jing-Na Si; Ren-Xiang Yan; Chuan Wang; Ziding Zhang; Xiao-Dong Su
Journal:  BMC Struct Biol       Date:  2009-12-14

10.  DescFold: a web server for protein fold recognition.

Authors:  Ren-Xiang Yan; Jing-Na Si; Chuan Wang; Ziding Zhang
Journal:  BMC Bioinformatics       Date:  2009-12-14       Impact factor: 3.169

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