Can sequence determine function?
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Corresponding authors: John A Gerlt j-gerlt@uiuc.edu - Patricia C Babbitt babbitt@cgl.ucsf.edu
Genome Biology 2000, 1:reviews0005-reviews0005.10 doi:10.1186/gb-2000-1-5-reviews0005
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BioMed Central: 15 citations
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Research article
Knowledge-based annotation of small molecule binding sites in proteins Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko, Thomas Madej BMC Bioinformatics 2010, 11:365 (1 July 2010) Protein-small molecule interactions can now be predicted with greater accuracy by a new algorithm on the web server IBIS that utilizes inference-by-homology to rank predicted binding sites based on their biological relevance.
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Methodology article
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning Adrian K Arakaki, Ying Huang, Jeffrey Skolnick BMC Bioinformatics 2009, 10:107 (13 April 2009) |
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Research
Gaëlle Lelandais, Véronique Tanty, Colette Geneix, Catherine Etchebest, Claude Jacq, Frédéric Devaux Genome Biology 2008, 9:R164 (24 November 2008) Comparative transcriptomics of |
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Research article
Valérie de Crécy-Lagard, Basma El Yacoubi, Rocío de la Garza, Alexandre Noiriel, Andrew D Hanson BMC Genomics 2007, 8:245 (23 July 2007) |
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Proceedings
CORRIE: enzyme sequence annotation with confidence estimates Benjamin Audit, Emmanuel D Levy, Wally R Gilks, Leon Goldovsky, Christos A Ouzounis BMC Bioinformatics 2007, 8(Suppl 4):S3 (22 May 2007) |
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Research article
High precision multi-genome scale reannotation of enzyme function by EFICAz Adrian K Arakaki, Weidong Tian, Jeffrey Skolnick BMC Genomics 2006, 7:315 (13 December 2006) |
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Software
Nandini Krishnamurthy, Duncan P Brown, Dan Kirshner, Kimmen Sjölander Genome Biology 2006, 7:R83 (14 September 2006) PhyloFacts, a structural phylogenomic database for protein functional and structural classification, is described. |
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Methodology article
Genome comparison using Gene Ontology (GO) with statistical testing Zhaotao Cai, Xizeng Mao, Songgang Li, Liping Wei BMC Bioinformatics 2006, 7:374 (11 August 2006) |
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Research article
Probabilistic annotation of protein sequences based on functional classifications Emmanuel D Levy, Christos A Ouzounis, Walter R Gilks, Benjamin Audit BMC Bioinformatics 2005, 6:302 (14 December 2005) |
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Minireview
Cross-species comparison of genome-wide expression patterns Xianghong Zhou, Greg Gibson Genome Biology 2004, 5:232 (21 June 2004) Recent studies have used cross-species comparisons of expression profiles to annotate gene functions, to draw evolutionary inferences concerning specific biological processes and to study the global properties of expression networks. |
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NSP Primer
TIM Barrels: One Structure with Diverse Functions Gregory A Petsko, Dagmar Ringe Protein Structure and Function 2003, $article.volume.volumeNumber:11-11 (20 May 2003) |
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Research
JEvTrace: refinement and variations of the evolutionary trace in JAVA Marcin P Joachimiak, Fred E Cohen Genome Biology 2002, 3:research0077-research0077.12 (26 November 2002) Protein families and phylogeny represent complex data with statistical outliers and special cases. The JEvTrace implementation of the evolutionary trace method in a JAVA graphical interface allows detailed mining and graphical visualization of evolutionary sequence relationships. |
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NSP Primer
TIM Barrels: One Structure with Diverse Function Gregory A Petsko, Dagmar Ringe Chapter 3 of Protein Structure and Function: From Sequence to Consequence 2002, $article.volume.volumeNumber:$article.firstPage (29 May 2002) |
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Deposited research article
Using orthologous and paralogous proteins to identify specificity determining residues Leonid A Mirny, Mikhail S Gelfand Genome Biology 2002, 3:preprint0002-preprint0002.20 (19 February 2002) Functional specificity of proteins is assumed to be conserved among orthologs and to be different among paralogs. We used this assumption to identify the residues that determine specificity of protein-DNA and protein-ligand recognition and present a method to compute the statistical significance of the predictions. |
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Correspondence
Orthologs and paralogs - we need to get it right Roy A Jensen Genome Biology 2001, 2:interactions1002-interactions1002.3 (3 August 2001) A response to Homologuephobia, by Gregory A Petsko, |