Literature DB >> 16731984

New avenues in protein function prediction.

Iddo Friedberg1, Martin Jambon, Adam Godzik.   

Abstract

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Year:  2006        PMID： 16731984      PMCID： PMC2242544          DOI： 10.1110/ps.062158406

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


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  10 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation.

Authors:  P W Lord; R D Stevens; A Brass; C A Goble
Journal:  Bioinformatics       Date:  2003-07-01       Impact factor: 6.937

Review 3.  Metagenomics: DNA sequencing of environmental samples.

Authors:  Susannah Green Tringe; Edward M Rubin
Journal:  Nat Rev Genet       Date:  2005-11       Impact factor: 53.242

4.  Enhanced automated function prediction using distantly related sequences and contextual association by PFP.

Authors:  Troy Hawkins; Stanislav Luban; Daisuke Kihara
Journal:  Protein Sci       Date:  2006-05-02       Impact factor: 6.725

5.  Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.

Authors:  David M Kristensen; Brian Y Chen; Viacheslav Y Fofanov; R Matthew Ward; Andreas Martin Lisewski; Marek Kimmel; Lydia E Kavraki; Olivier Lichtarge
Journal:  Protein Sci       Date:  2006-05-02       Impact factor: 6.725

6.  A categorization approach to automated ontological function annotation.

Authors:  Karin Verspoor; Judith Cohn; Susan Mniszewski; Cliff Joslyn
Journal:  Protein Sci       Date:  2006-05-02       Impact factor: 6.725

7.  Functional annotation prediction: all for one and one for all.

Authors:  Ori Sasson; Noam Kaplan; Michal Linial
Journal:  Protein Sci       Date:  2006-05-02       Impact factor: 6.725

Review 8.  The impact of structural genomics: expectations and outcomes.

Authors:  John-Marc Chandonia; Steven E Brenner
Journal:  Science       Date:  2006-01-20       Impact factor: 47.728

9.  Structure-based function inference using protein family-specific fingerprints.

Authors:  Deepak Bandyopadhyay; Jun Huan; Jinze Liu; Jan Prins; Jack Snoeyink; Wei Wang; Alexander Tropsha
Journal:  Protein Sci       Date:  2006-06       Impact factor: 6.725

10.  Improving the precision of the structure-function relationship by considering phylogenetic context.

Authors:  Boris E Shakhnovich
Journal:  PLoS Comput Biol       Date:  2005-06-24       Impact factor: 4.475
  10 in total
  16 in total

1.  Structure- and sequence-based function prediction for non-homologous proteins.

Authors:  Lee Sael; Meghana Chitale; Daisuke Kihara
Journal:  J Struct Funct Genomics       Date:  2012-01-22

2.  Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones.

Authors:  Dao Feng Xiang; Peter Kolb; Alexander A Fedorov; Chengfu Xu; Elena V Fedorov; Tamari Narindoshivili; Howard J Williams; Brian K Shoichet; Steven C Almo; Frank M Raushel
Journal:  Biochemistry       Date:  2012-02-15       Impact factor: 3.162

3.  ESG: extended similarity group method for automated protein function prediction.

Authors:  Meghana Chitale; Troy Hawkins; Changsoon Park; Daisuke Kihara
Journal:  Bioinformatics       Date:  2009-05-12       Impact factor: 6.937

Review 4.  FINDSITE: a combined evolution/structure-based approach to protein function prediction.

Authors:  Jeffrey Skolnick; Michal Brylinski
Journal:  Brief Bioinform       Date:  2009-03-26       Impact factor: 11.622

5.  Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.

Authors:  Jennifer A Cummings; Alexander A Fedorov; Chengfu Xu; Shoshana Brown; Elena Fedorov; Patricia C Babbitt; Steven C Almo; Frank M Raushel
Journal:  Biochemistry       Date:  2009-07-14       Impact factor: 3.162

6.  Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP.

Authors:  Troy Hawkins; Meghana Chitale; Daisuke Kihara
Journal:  BMC Bioinformatics       Date:  2010-05-19       Impact factor: 3.169

Review 7.  The eukaryotic flagellum makes the day: novel and unforeseen roles uncovered after post-genomics and proteomics data.

Authors:  Michely C Diniz; Ana Carolina L Pacheco; Kaio M Farias; Diana M de Oliveira
Journal:  Curr Protein Pept Sci       Date:  2012-09       Impact factor: 3.272

8.  A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

Authors:  Yuzhen Ye; Thomas G Doak
Journal:  PLoS Comput Biol       Date:  2009-08-14       Impact factor: 4.475

9.  In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment.

Authors:  Meghana Chitale; Ishita K Khan; Daisuke Kihara
Journal:  BMC Bioinformatics       Date:  2013-02-28       Impact factor: 3.169

10.  Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.

Authors:  Mart Krupovic; Mathieu Gonnet; Wajdi Ben Hania; Patrick Forterre; Gaël Erauso
Journal:  PLoS One       Date:  2013-01-11       Impact factor: 3.240
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