Pathways databases

The tutorial in Section 10.3.1.8 presents some of the various ways the information in the Biochemical Pathways database can be retrieved. In this tutorial the importance of searching for the reaction center, the atoms and bonds directly involved in the bond rearrangement scheme, is emphasized, It is a prerequisite for getting a deeper understanding of chemical reactions. 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

The 3D pharmacophore search with C(5)ROL in the Biochemical Pathways database provided 13 different molecules as hits. To further limit the number of hits, the additional restriction was imposed that the hits should have only two hydrogen... 

These examples served to show that the Biochemical Pathways database provides a rich source of information on these all important reactions that determine the transformation of nutrients into the broad spectrum of compounds contained in living species and the concomitant production of energy to keep these processes going. 

Development of multidimension pathway databases Current database tools do not encompass the true complexities of plants. In this regard, multidimensional databases need to be developed to integrate allelic variation with temporal, developmental, tissue-specific, and biotic and abiotic influences on pathway flux and pigment accumulation. 

OGATA, H., GOTO, S., FUJIBUCHI, W., KANEHISA, M., Computation with the KEGG pathway database, BioSystems, 1998,47,119-128. 

Useful Resources and Webpages to Assemble Information on Kinetic Models, Including Pathway Databases and Model Repositories... 

Alzheimer s disease. Some other pathway databases, such as the Human Protein Reference Database (HPRD) and Reactome, are also listed in Table 1.3. 

Biologists have not only organized the cell into pathways and modules but also classified these pathways into various types. Each of the main types has a different computational representation in pathway databases. Bader and Enright (2005) discussed three biochemical- and biophysical-based pathways that are modeled ... 

Identifying constraints on reaction directions is essential for applications of metabolic flux analysis. However, in many applications the procedure used for determining reaction directions is not concretely defined. Typically, a subset of the reactions in a model is assigned as irreversible and the feasible directions are assigned based on information in pathway databases [59], In these applications, by treating certain reactions as implicitly unidirectional, biologically reasonable results can often be obtained without considering the system thermodynamics as outlined above. 

The World Wide Web Virtual Library Biosciences points to virtual library pages for Biological Molecules, and Biochemistry and Molecular Biology. Each of these pages presents a long list of Web resources. The World Wide Web Virtual Library Biological Molecules covers molecular sequence and structure databases, metabolic pathway databases, and other lists of Web resources. The World Wide Web Virtual library Biochemistry and Molecular Biology is a list of resources, listed by provider. 

Green ML, Karp PD. The outcomes of pathway database com- 14. putations depend on pathway ontology. Nucleic Acids Res. 2006 34 3687-3697. 

Table 1 Some representative metabolic pathway databases...

The analysis of network structure from the viewpoint of computer theory requires an introduction to some background information, which will be provided here. We will introduce the data involved for modeling metabolic pathways and the KEGG pathway database in particular. Furthermore, a basic introduction to graphs as used in computer science will be provided. 

KEGG http //www. genome. jp /kegg/pathway.html A pathway database... 

H. Ogata, S. Goto, W. Eujibuchi, and M. Kanehisa, Computation with the KEGG pathway database. Biosystems 47(1-2) 119-128 (1998). 

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