Nucleic Acids Research · 2010 · 275 citations · 11 references
Life SciencesBiochemistryBioinformaticsMetabolismMicrobial MetabolismPathway AnalysisBiotransformation PathwaysMetabolic Pathway AnalysisMetabolic PathwaysPathway AnnotationPathway DatabasesReaction PathwaysBiochemical Pathway DatabasesEnzyme NomenclatureGlobal AlignmentMetabolic Pathway DatabasesMetabolic Pathway DiscoveryMicrobial BiodegradationReaction Pathway DatabasesSecondary Metabolites
The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred (http://www.genome.jp/tools/pathpred/), a web-based server to predict plausible pathways of muti-step reactions starting from a query compound, based on the local RDM pattern match and the global chemical structure alignment against the reactant pair library. In this server, we focus on predicting pathways for microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites, which correspond to characteristic RDM patterns in 947 and 1397 reactant pairs, respectively. The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph.
11
KAAS: an automatic genome annotation and pathway reconstruction server
Yuki Moriya, Masumi Itoh, Shujiro Okuda et al. · Nucleic Acids Research · 2007 · 4.3K citations · Full text
Masahiro Hattori, Yasushi Okuno, Susumu Goto et al. · Journal of the American Chemical Society · 2003 · 492 citations