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EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes.

Kumar N, Skolnick J.

Bioinformatics. 2012 Oct 15;28(20):2687-8. doi: 10.1093/bioinformatics/bts510.


EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.

Arakaki AK, Huang Y, Skolnick J.

BMC Bioinformatics. 2009 Apr 13;10:107. doi: 10.1186/1471-2105-10-107.


High precision multi-genome scale reannotation of enzyme function by EFICAz.

Arakaki AK, Tian W, Skolnick J.

BMC Genomics. 2006 Dec 13;7:315.


EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.

Tian W, Arakaki AK, Skolnick J.

Nucleic Acids Res. 2004 Dec 1;32(21):6226-39.


PSiFR: an integrated resource for prediction of protein structure and function.

Pandit SB, Brylinski M, Zhou H, Gao M, Arakaki AK, Skolnick J.

Bioinformatics. 2010 Mar 1;26(5):687-8. doi: 10.1093/bioinformatics/btq006.


CORRIE: enzyme sequence annotation with confidence estimates.

Audit B, Levy ED, Gilks WR, Goldovsky L, Ouzounis CA.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S3.


dbCAN: a web resource for automated carbohydrate-active enzyme annotation.

Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W445-51. doi: 10.1093/nar/gks479.


EnzymeDetector: an integrated enzyme function prediction tool and database.

Quester S, Schomburg D.

BMC Bioinformatics. 2011 Sep 23;12:376. doi: 10.1186/1471-2105-12-376.


Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases.

Yu C, Zavaljevski N, Desai V, Reifman J.

Proteins. 2009 Feb 1;74(2):449-60. doi: 10.1002/prot.22167.


CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC.

Glycobiology. 2010 Dec;20(12):1574-84. doi: 10.1093/glycob/cwq106.


BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation.

Bannert C, Welfle A, Aus dem Spring C, Schomburg D.

BMC Bioinformatics. 2010 Dec 1;11:589. doi: 10.1186/1471-2105-11-589.


DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.

Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T.

BMC Bioinformatics. 2015 Mar 21;16:96. doi: 10.1186/s12859-015-0499-y.


Bioverse: Functional, structural and contextual annotation of proteins and proteomes.

McDermott J, Samudrala R.

Nucleic Acids Res. 2003 Jul 1;31(13):3736-7.


Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

Ramkissoon KR, Miller JK, Ojha S, Watson DS, Bomar MG, Galande AK, Shearer AG.

PLoS One. 2013 Dec 30;8(12):e84508. doi: 10.1371/journal.pone.0084508.


DETECT--a density estimation tool for enzyme classification and its application to Plasmodium falciparum.

Hung SS, Wasmuth J, Sanford C, Parkinson J.

Bioinformatics. 2010 Jul 15;26(14):1690-8. doi: 10.1093/bioinformatics/btq266.


Version VI of the ESTree db: an improved tool for peach transcriptome analysis.

Lazzari B, Caprera A, Vecchietti A, Merelli I, Barale F, Milanesi L, Stella A, Pozzi C.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S9. doi: 10.1186/1471-2105-9-S2-S9.


pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.

Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L.

Bioinformatics. 2013 May 1;29(9):1215-7. doi: 10.1093/bioinformatics/btt129.


ORENZA: a web resource for studying ORphan ENZyme activities.

Lespinet O, Labedan B.

BMC Bioinformatics. 2006 Oct 6;7:436.


CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X.

BMC Genomics. 2012 Dec 20;13:715. doi: 10.1186/1471-2164-13-715.

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