Literature DB >> 16187357

SPARKS 2 and SP3 servers in CASP6.

Hongyi Zhou1, Yaoqi Zhou.   

Abstract

Two single-method servers, SPARKS 2 and SP3, participated in automatic-server predictions in CASP6. The overall results for all as well as detailed performance in comparative modeling targets are presented. It is shown that both SPARKS 2 and SP3 are able to recognize their corresponding best templates for all easy comparative modeling targets. The alignment accuracy, however, is not always the best among all the servers. Possible factors are discussed. SPARKS 2 and SP3 fold recognition servers, as well as their executables, are freely available for all academic users on http://theory.med.buffalo.edu. 2005 Wiley-Liss, Inc.

Entities:  

Mesh：

Year:  2005        PMID： 16187357     DOI： 10.1002/prot.20732

Source DB:  PubMed          Journal:  Proteins        ISSN： 0887-3585


  36 in total

1.  Improving threading algorithms for remote homology modeling by combining fragment and template comparisons.

Authors:  Hongyi Zhou; Jeffrey Skolnick
Journal:  Proteins       Date:  2010-07

2.  Template-based protein structure modeling using TASSER(VMT.).

Authors:  Hongyi Zhou; Jeffrey Skolnick
Journal:  Proteins       Date:  2011-11-22

3.  Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana.

Authors:  Tao Lu; Yuedong Yang; Bo Yao; Song Liu; Yaoqi Zhou; Chi Zhang
Journal:  Protein Sci       Date:  2012-05-01       Impact factor: 6.725

4.  Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction.

Authors:  Huiying Zhao; Yuedong Yang; Yaoqi Zhou
Journal:  RNA Biol       Date:  2011-11-01       Impact factor: 4.652

5.  Sub-AQUA: real-value quality assessment of protein structure models.

Authors:  Yifeng David Yang; Preston Spratt; Hao Chen; Changsoon Park; Daisuke Kihara
Journal:  Protein Eng Des Sel       Date:  2010-06-04       Impact factor: 1.650

6.  Ab initio protein structure prediction using chunk-TASSER.

Authors:  Hongyi Zhou; Jeffrey Skolnick
Journal:  Biophys J       Date:  2007-05-11       Impact factor: 4.033

7.  Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential.

Authors:  Hongyi Zhou; Jeffrey Skolnick
Journal:  Proteins       Date:  2008-05-15

8.  Protein structure prediction by pro-Sp3-TASSER.

Authors:  Hongyi Zhou; Jeffrey Skolnick
Journal:  Biophys J       Date:  2009-03-18       Impact factor: 4.033

9.  Black mamba venom peptides target acid-sensing ion channels to abolish pain.

Authors:  Sylvie Diochot; Anne Baron; Miguel Salinas; Dominique Douguet; Sabine Scarzello; Anne-Sophie Dabert-Gay; Delphine Debayle; Valérie Friend; Abdelkrim Alloui; Michel Lazdunski; Eric Lingueglia
Journal:  Nature       Date:  2012-10-03       Impact factor: 49.962

10.  Lipid transfer proteins in coffee: isolation of Coffea orthologs, Coffea arabica homeologs, expression during coffee fruit development and promoter analysis in transgenic tobacco plants.

Authors:  Michelle G Cotta; Leila M G Barros; Juliana D de Almeida; Fréderic de Lamotte; Eder A Barbosa; Natalia G Vieira; Gabriel S C Alves; Felipe Vinecky; Alan C Andrade; Pierre Marraccini
Journal:  Plant Mol Biol       Date:  2014-01-28       Impact factor: 4.076
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