Bioinformatics Integration Framework for Metabolic Pathway Data-Mining. T Arredondo V,M Seeger P,L Dombrovskaia,J Avarias A,F Calderon B,D Candel C,F Munoz R,V Latorre R,L Agullo,M Cordova H. Lecture Notes in Computer Science . 2006...
Karp P.D. The MetaCyc Metabolic Pathway Databasein Metabolic Engineering, Horizon Scientific Press, 2003. ↓ Review online Read more from SRI December 5, 2024 2024 at SRI: A year of breakthroughs Delivering world-changing solutions for a safer, healthier, and more sustainable future. December...
Using the MetaCyc pathway database and the BioCyc database collection. The MetaCyc database (http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the l... R Caspi,PD Karp - 《Current Protocols in Bioinformatics》...
In addition, the cell behavior can be studied by modeling the cellular context.We have implemented a Monte Carlo algorithm (DESHARKY) that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism ...
One of the current challenges in bioinformatics is to discover new ways to transform a set of compounds into specific products. The usual approach is finding the reactions to synthesize a particular product, from a given substrate, by means of classical
KEGG PATHWAY analysis represents molecular interaction, reaction and relation networks in metabolism, cellular process, human disease, drug discovery, etc. It is a reference database for metabolic pathway analysis also. So, we performed KEGG pathway analysis for weighted differentially coexpressed gene ...
The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale ...
KEGG pathway database - Kyoto University Bioinformatics Centre. [http://www.genome.jp/kegg/pathway.html], BioModels Database. [http://www.ebi.ac.uk/biomodels], MetaCyc Encyclopedia of Metabolic Pathways. [http://metacyc.org], Sridhar P, Kahveci T, Ranka S:An iterative algorithm for metab...
Caspi R, Karp PD: Using the MetaCyc pathway database and the BioCyc database collection. Curr Protoc Bioinformatics 2007., Chapter 1(Unit1 17): Book Google Scholar Haft DH, Paulsen IT, Ward N, Selengut JD: Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTER...
in that the resultant-directed metabolic networks are generated without the bias created by mapping metabolite data onto a pathway's pre-existing structure (Easton, 2013). The collection of all chemical events that occur within a live creature to preserve life is depicted graphically by metabolic ...