论文信息 - Enabling the exploration of biochemical pathways.

Enabling the exploration of biochemical pathways.

The Biochemical Pathways Wall Chart (http://www.expasy.org/tools/pathways/ref.1) has been converted into a molecule and reaction database. Major features of this database are that each molecule is represented by lists of all atoms and bonds (as connection tables), and in the reactions the reaction centre, the atoms and bonds directly involved in the bond rearrangement process, are marked. The information in the database has been enriched by a set of diverse 3D structure conformations generated by the programs CORINA and ROTATE. The web-based structure and reaction retrieval system C@ROL provides a wide range of search methods to mine this rich database. The database is accessible at http://www2.chemie.uni-erlangen.de/services/biopath/index.html and http://www.mol-net.de/databases/biopath.html .

J. Gasteiger | Martin Reitz | O. Sacher | A. Tarkhov | D. Trumbach

[1] Masanori Arita. The metabolic world of Escherichia coli is not small. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[2] J. Thornton,et al. A structure-based anatomy of the E.coli metabolome. , 2003, Journal of molecular biology.

[3] Susumu Goto,et al. LIGAND: database of chemical compounds and reactions in biological pathways , 2002, Nucleic Acids Res..

[4] Peter D. Karp,et al. The MetaCyc Database , 2002, Nucleic Acids Res..

[5] Gerhard Klebe,et al. Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures , 1994, J. Chem. Inf. Comput. Sci..

[6] Wolf-Dietrich Ihlenfeldt,et al. Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and compatibility , 1994, J. Chem. Inf. Comput. Sci..

[7] Linus Pauling,et al. Molecular Architecture and Biological Reactions , 1946 .