Predictive genomic and metabolomic analysis for the standardization of enzyme data

Acker, 2014, Considerations for the design and reporting of enzyme assays in high-throughput screening applications, Perspect. Sci., 1, 56, 10.1016/j.pisc.2013.12.001 Apweiler, 2001, The InterPro database, an integrated documentation resource for protein families, domains and functional sites, Nucleic Acids Res., 29, 37, 10.1093/nar/29.1.37 Bairoch, 2000, The ENZYME database in 2000, Nucleic Acids Res., 28, 304, 10.1093/nar/28.1.304 Bairoch, 1991, PROSITE: a dictionary of sites and patterns in proteins, Nucleic Acids Res., 19, 2241, 10.1093/nar/19.suppl.2241 Bairoch, 1991, The SWISS-PROT protein sequence data bank, Nucleic Acids Res., 19, 2247, 10.1093/nar/19.suppl.2247 Barker, 1999, The Protein Information Resource (PIR), Nucleic Acids Res., 28, 41, 10.1093/nar/28.1.41 Bernstein, 1977, The protein data bank: a computer-based archival file for macromolecular structures, J. Mol. Biol., 112, 535, 10.1016/S0022-2836(77)80200-3 Carter, 1986, Site-directed mutagenesis, Biochem. J., 237, 1, 10.1042/bj2370001 Chen, 2005, ChemDB: a public database of small molecules and related chemoinformatics resources, Bioinformatics, 21, 4133, 10.1093/bioinformatics/bti683 Dayhoff, 1973 Dry, 2000, Structural genomics in the biotechnology sector, Nat. Struct. Mol. Biol., 7, 946, 10.1038/80718 Ghirlanda, 2008, Old enzymes, new tricks, Nature, 453, 164, 10.1038/453164a Goad, 1987, Computational tools for using and analyzing DNA sequences, Somatic Cell Mol. Genet., 13, 391, 10.1007/BF01534937 Handelsman, 2004, Metagenomics: application of genomics to uncultured microorganisms, Microbiol. Mol. Biol. Rev., 68, 669, 10.1128/MMBR.68.4.669-685.2004 Hashimoto, 2009, Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans, Carbohydr. Res., 344, 881, 10.1016/j.carres.2009.03.001 Hashimoto, 2008, The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes, J. Lipid Res., 49, 183, 10.1194/jlr.M700377-JLR200 Hattori, 2011, Chemoinformatics on metabolic pathways: attaching biochemical information on putative enzymatic reactions, 318 Hattori, 2003, Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways, J. Am. Chem. Soc., 125, 11853, 10.1021/ja036030u Holm, 1994, The FSSP database of structurally aligned protein fold families, Nucleic Acids Res., 22, 3600 Kanehisa, 2010, KEGG for representation and analysis of molecular networks involving diseases and drugs, Nucleic Acids Res., 38, D355, 10.1093/nar/gkp896 Kanehisa, 2008, KEGG for linking genomes to life and the environment, Nucleic Acids Res., 36, D480, 10.1093/nar/gkm882 Kanehisa, 2002, The KEGG databases at GenomeNet, Nucleic Acids Res., 30, 42, 10.1093/nar/30.1.42 Kawano, 2005, Prediction of glycan structures from gene expression data based on glycosyltransferase reactions, Bioinformatics, 21, 3976, 10.1093/bioinformatics/bti666 Kotera, 2008, Eliciting possible reaction equations and metabolic pathways involving orphan metabolites, J. Chem. Inf. Model., 48, 2335, 10.1021/ci800213g Kotera, 2004, Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions, J. Am. Chem. Soc., 126, 16487, 10.1021/ja0466457 Marchler-Bauer, 2002, CDD: a curated Entrez database of conserved domain alignments, Nucleic Acids Res., 31, 383, 10.1093/nar/gkg087 Monasterio, 2014, Nomenclature for the applications of nuclear magnetic resonance to the study of enzymes, Perspect. Sci., 1, 88, 10.1016/j.pisc.2014.02.007 Minowa, 2007, Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes, J. Mol. Biol., 368, 1500, 10.1016/j.jmb.2007.02.099 Moriya, 2010, PathPred: an enzyme-catalyzed metabolic pathway prediction server, Nucleic Acids Res., 38, W138, 10.1093/nar/gkq318 Murzin, 1995, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol., 247, 536, 10.1016/S0022-2836(05)80134-2 Nishikawa, 1993, Constructing a protein mutant database, Protein Eng., 7, 733, 10.1093/protein/7.5.733 Oh, 2007, Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways, J. Chem. Inf. Model., 47, 1702, 10.1021/ci700006f Orengo, 1997, CATH – a hierarchic classification of protein domain structures, Structure, 5, 1093, 10.1016/S0969-2126(97)00260-8 Payen, 1833, Mémoire sur la diastase, les principaux produits de ses réactions et leurs applications aux arts industriels, Ann. Chim. Phys., 53, 73 Raes, 2008, Molecular eco-systems biology: towards an understanding of community function, Nat. Rev. Microbiol., 6, 693, 10.1038/nrmicro1935 Riesenfeld, 2004, METAGENOMICS: genomic analysis of microbial communities, Ann. Rev. Genet., 38, 525, 10.1146/annurev.genet.38.072902.091216 Sanger, 1951, The amino-acid sequence in the phenylalanyl chain of insulin. I. The identification of lower peptides from partial hydrolysates, Biochem. J., 49, 463, 10.1042/bj0490463 Sanger, 1951, The amino-acid sequence in the phenylalanyl chain of insulin. 2. The investigation of peptides from enzymic hydrolysates, Biochem. J., 49, 481, 10.1042/bj0490481 Schloss, 2003, Biotechnological prospects from metagenomics, Curr. Opin. Biotechnol., 14, 303, 10.1016/S0958-1669(03)00067-3 Sonnhammer, 1997, Pfam: a comprehensive database of protein domain families based on seed alignments, PROTEINS: Struct. Funct. Genet., 28, 405, 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L Tipton, 2000, History of the enzyme nomenclature system, Bioinformatics, 16, 34, 10.1093/bioinformatics/16.1.34 Tringe, 2005, Comparative metagenomics of microbial communities, Science, 308, 554, 10.1126/science.1107851 Turnbaugh, 2008, An invitation to the marriage of metagenomics and metabolomics, Cell, 134, 708, 10.1016/j.cell.2008.08.025 Yamanishi, 2009, E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate–product pairs, Bioinformatics, 25, i79, 10.1093/bioinformatics/btp223