• MetaCyc

  • Referenced in 27 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 8 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...
  • TRANSPATH

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

  • Referenced in 7 articles [sw22589]
  • such as molecular structure, neurobiology and metabolic pathway engineering, and is rapidly emerging...
  • 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...
  • 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...
  • HMDB

  • Referenced in 7 articles [sw28995]
  • diagrams for  25,000 human metabolic and disease pathways, while FooDB contains equivalent information...
  • Cell Illustrator

  • Referenced in 4 articles [sw06594]
  • moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways...
  • 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...
  • WebGestalt

  • Referenced in 7 articles [sw17514]
  • tissue expression pattern, chromosome distribution, metabolic and signaling pathways, protein domain information and publications...
  • SBML-PET

  • Referenced in 2 articles [sw12829]
  • signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export...
  • GASCO

  • Referenced in 2 articles [sw28664]
  • responses and synthetic gene design for metabolic pathway engineering. The software for the proposed algorithm...
  • Gene3D

  • Referenced in 2 articles [sw22981]
  • sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG...