One of the greatest challenges in bioinformatics is to shed light on the relationship between genomic and chemical significances of metabolic pathways. Here, we demonstrate two types of chemical structure search servers: SIMCOMP (http://www.genome.jp/tools/simcomp/) for the chemical similarity search and SUBCOMP (http://www.genome.jp/tools/subcomp/) for the chemical substructure search, where both servers provide links to the KEGG PATHWAY and BRITE databases. The SIMCOMP is a graph-based method for searching the maximal common subgraph isomorphism by finding the maximal cliques in the association graph. In contrast, the SUBCOMP is an extended method for solving the subgraph isomorphism problem. The obtained links to PATHWAY or BRITE databases can be used to interpret as the biological meanings of chemical structures from the viewpoint of the various biological functions including metabolic networks.
The XyM notation system is proposed as a linear notation for the electronic communication of structural formulas. Each XyM notation consists of a skeleton with such arguments as SUBSLIST, ATOMLIST, and BONDLIST. The arguments are designed to be capable of carrying out substitution derivation for placing large substituents, atom derivation for spiro fusion, and bond derivation for ring fusion. Additional arguments, SKBONDLIST and OMITLIST, are discussed for stereochemical and ring-opening information. The XyM notation system is implemented as a LaTeX2e application.
We present a SAR method that can predict estrogen-like endocrine disrupting chemical (EDC) activity as well as key biodegradation steps for detoxification. This method is based on a recent graph-mining algorithm developed by Kudo et al., which generates a set of descriptors from all potent chemical fragments (including rings). This method is novel in that it achieves chemical diversity in the training data set by sampling another data set of larger diversity. The model achieved an 83% accuracy prediction rate, and identified 1291 EDC candidates from the KEGG database. From this set of candidate compounds, bisphenol A was chosen for assay validation and biodegradation pathway analysis. Results showed that bisphenol A exhibited estrogen-like activity and was degraded in three distinct reactions. The prediction model provided information on the mechanism of the ligand-target binding, such as key functional groups involved. We focused on the enzyme commission number, which is useful for analyses of biodegradation pathways. Results identified oxygenases, ether hydrolases, and carbon-halide lyases as being important in the biodegradation pathway. This combined approach provided new information regarding the biodegradation of EDCs, and can potentially be extended to applications with transcriptomic, proteomic, and metabolomic data to provide a quick screen of biological activity and biodegradation pathway(s).
The XyMJava system for drawing chemical structural formulas has been developed by using the Java language in order to enhance World Wide Web communication of chemical information, where the XyM notation system proposed previously has been adopted as a language for inputting structural data. The object-oriented technique, especially the design-pattern approach, is applied to parse a XyM notation in the XyMJava system. A chemical model is introduced to encapsulate information on chemical structural formulas and used to draw the formula on a CRT display. Thereby, an HTML document containing a XyM notation can be browsed by the XyMApplet of the XyM Java system.
The XyM2Mol system, which consists of the XyM2Mol application and the XyM2Mol applet, is developed to convert XyM-notation codes into connection tables. Thereby, the structural data by XyM Notation become applicable to a wide variety of chemical applications through such connection tables.
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