• MetaCyc

  • Referenced in 29 articles [sw08243]
  • database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 2097 pathways from more ... literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated ... universe of metabolism by storing a representative sample of each experimentally elucidated pathway. MetaCyc ... data set for computationally predicting the metabolic pathways of organisms from their sequenced genomes, supporting...
  • SCAMP

  • Referenced in 11 articles [sw02112]
  • facilities, including: the ability to describe metabolic pathways of any structure and possessing any kinetics ... access to all coefficients and elasticities of metabolic control analysis; user-defined forcing functions...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • used to browse model content, visualize metabolic pathway maps, and export SBML files ... have access to high quality curated metabolic models and reconstructions. It is freely available...
  • Virtual Cell

  • Referenced in 9 articles [sw22589]
  • such as molecular structure, neurobiology and metabolic pathway engineering, and is rapidly emerging...
  • TRANSPATH

  • Referenced in 7 articles [sw08272]
  • database of mammalian signal transduction and metabolic pathways. As one of the earliest pathway databases...
  • COXPRESdb

  • Referenced in 7 articles [sw41318]
  • gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases...
  • Cell Illustrator

  • Referenced in 6 articles [sw06594]
  • moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways...
  • StSNP

  • Referenced in 3 articles [sw30039]
  • protein structures with linkage to metabolic pathways. SNPs located within the open reading frame ... increasing/decreasing the activity of the metabolic pathway. Understanding the functional consequences of such changes ... modeling of nsSNPs with links to metabolic pathway information, along with real-time visual comparative ... Friend software application. The use of metabolic pathways in StSNP allows a researcher to examine...
  • SubMAP

  • Referenced in 3 articles [sw25790]
  • SubMAP: Aligning metabolic pathways with subnetwork mappings. We consider the problem of aligning two metabolic ... algorithm SubMAP (Subnetwork Mappings in Alignment of Pathways). We evaluate its accuracy and performance ... observe that SubMAP is scalable for metabolic pathways of arbitrary topology, including searching...
  • HMDB

  • Referenced in 9 articles [sw28995]
  • diagrams for  25,000 human metabolic and disease pathways, while FooDB contains equivalent information...
  • WinBEST-KIT

  • Referenced in 5 articles [sw35398]
  • complicated biochemical reaction systems such as metabolic pathways. WinBEST-KIT provides an integrated simulation environment...
  • Graemlin

  • Referenced in 5 articles [sw29736]
  • topologies other than protein complexes and metabolic pathways. To assess Græmlin’s performance, we have...
  • MetaModel

  • Referenced in 4 articles [sw09011]
  • modelling and control analysis of metabolic pathways on the IBM PC and compatibles. MetaModel ... steady-state fluxes and metabolite concentrations of metabolic systems on the IBM PC and compatible ... calculate the control structure of a pathway: it provides not only an educational tool that ... verify empirically the classic summation relationships of metabolic control analysis but also a research tool...
  • CoMeta

  • Referenced in 2 articles [sw25789]
  • Comparing metabolic pathways through reactions and potential fluxes. Comparison of metabolic pathways is useful ... techniques have been proposed to compare metabolic pathways. Most of them focus on structural aspects ... propose a new method for comparing metabolic pathways of different organisms based on a similarity...
  • Gaggle

  • Referenced in 4 articles [sw20341]
  • associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource...
  • MMG

  • Referenced in 4 articles [sw29328]
  • probabilistic tool to identify submodules of metabolic pathways. MOTIVATION: A fundamental task in systems biology...
  • SMPDB

  • Referenced in 2 articles [sw29378]
  • designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems ... fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways...
  • iPath

  • Referenced in 3 articles [sw16937]
  • iPath: interactive exploration of biochemical pathways and networks. iPath is an open-access online tool ... pathways.embl.de) for visualizing and analyzing metabolic pathways. An interactive viewer provides straightforward navigation through various ... underlying chemicals and enzymes. Customized pathway maps can be generated and annotated using various external ... pinpoint the complementarity of the host–symbiont metabolic capacities...
  • iMPTCE-Hnetwork

  • Referenced in 1 article [sw39601]
  • Hnetwork: a multilabel classifier for identifying metabolic pathway types of chemicals and enzymes with ... heterogeneous network. Metabolic pathway is an important type of biological pathways. It produces essential molecules ... life of living organisms. Each metabolic pathway consists of a chain of chemical reactions, which ... major components for each metabolic pathway. Although several metabolic pathways have been uncovered, the metabolic...
  • RelEx

  • Referenced in 7 articles [sw35376]
  • Motivation: The discovery of regulatory pathways, signal cascades, metabolic processes or disease models requires knowledge...