> Tag > Links tagged with 'metabolic networks and pathways'

Links tagged with 'metabolic networks and pathways'

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Found 21 links

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BioMet ToolboxTool Content

http://www.sysbio.se/BioMet [open in a new window]

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Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
BioMet Toolbox: genome-wide analysis of metabolism201017
NAR Web Server Issue 2010
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tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

BRENDADatabase Content

http://www.brenda-enzymes.org [open in a new window]

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Protein > Databases

The BRENDA (BRaunschweig ENzyme Database) enzyme information system is a collection of enzyme functional and property data, manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. A ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps.

This content is being maintained by Dietmar Schomburg.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
BRENDA, the enzyme information system in 2011201160
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsenzymes ligands metabolic networks and pathways protein conformation protein databases

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de [open in a new window]

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Human Genome > Databases
Model Organisms > Databases
Protein > Databases

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
ConsensusPathDB: toward a more complete picture of cell biology201115
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals factual databases gene expression gene regulatory networks genetic databases humans metabolic networks and pathways mice protein interaction mapping signal transduction

CPA - Comparative Pathway AnalyzerTool Content

https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html [open in a new window]

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Expression > Networks
Model Organisms > Microbes
Protein > Networks & Interactions, Pathways and Enzymes

The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms20087
NAR Web Server Issue 2008
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tagscluster analysis factual databases metabolic networks and pathways

FMMTool Content

http://FMM.mbc.nctu.edu.tw/ [open in a new window]

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
FMM: a web server for metabolic pathway reconstruction and comparative analysis200911
NAR Web Server Issue 2009
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tagsbacteria factual databases metabolic networks and pathways pharmaceutical preparations plants

FragmentStoreDatabase Content

http://bioinformatics.charite.de/fragment_store [open in a new window]

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Other Molecules > Databases

FragmentStore, a resource for the comparison of fragments found in metabolites, drugs or toxic compounds. Starting from 13,000 metabolites, 16,000 drugs and 2200 toxic compounds we generated 35,000 different building blocks (fragments), which are not only relevant to their biosynthesis and degradation but also provide important information regarding side-effects and toxicity. The FragmentStore provides a variety of search options such as 2D structure, molecular weight, rotatable bonds, etc. Various analysis tools have been implemented including the calculation of amino acid preferences of fragments' binding sites, classification of fragments based on the enzyme classification class of the enzyme(s) they bind to and small molecule library generation via a fragment-assembler tool.

This content is being maintained by robertpreissner.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
FragmentStore--a comprehensive database of fragments linking metabolites, toxic molecules and drugs20111
NAR Database Issue 2011
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tagsbinding sites drug design drug toxicity factual databases metabolic networks and pathways pharmaceutical preparations

GLAMMTool Content

http://glamm.lbl.gov [open in a new window]

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

GLAMM is a web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of novel, transgenic pathways.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
GLAMM: Genome-Linked Application for Metabolic Maps20115
NAR Web Server Issue 2011
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tagsgenomics metabolic networks and pathways

Gramene database in 2010Database Content

http://www.gramene.org [open in a new window]

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Model Organisms > Databases

The Gramene database has become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene has an Ensembl genome browser and host a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database.

links directory index: 25
TitlePublication YearGoogle Scholar Citation Count
Gramene database in 2010: updates and extensions201125
NAR Database Issue 2011
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tagschromosome mapping genetic databases genetic variation genomics metabolic networks and pathways plant genes plant genome plants quantitative trait loci synteny

HMDBDatabase Content

http://www.hmdb.ca/ [open in a new window]

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Human Genome > Other Resources
Other Molecules > Metabolites

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
Metabolomics: the principles and potential applications to transplantation200573
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tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance factual databases humans internet magnetic resonance spectroscopy mass spectrometry metabolic diseases metabolic networks and pathways metabolism metabolome organ transplantation quality control user-computer interface

InterProDatabase Content

http://www.ebi.ac.uk/interpro/index.html [open in a new window]

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Protein > Domains and Motifs

Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.

links directory index: 3869
TitlePublication YearGoogle Scholar Citation Count
InterPro in 2011: new developments in the family and domain prediction database201211
The InterPro BioMart: federated query and web service access to the InterPro Resource20114
InterPro: the integrative protein signature database2009585
New developments in the InterPro database2007392
InterPro, progress and status in 20052005562
The InterPro Database, 2003 brings increased coverage and new features2003700
InterPro: an integrated documentation resource for protein families, domains and functional sites200299
The InterPro database, an integrated documentation resource for protein families, domains and functional sites2001758
InterPro--an integrated documentation resource for protein families, domains and functional sites2000758
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tagsalgorithms amino acid repetitive sequences animals computational biology factual databases humans information services metabolic networks and pathways post-translational protein processing protein databases protein sequence analysis proteins search engine sequence alignment systems integration tertiary protein structure

iPathTool Content

http://pathways.embl.de [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

iPath is a web tool for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
iPath2.0: interactive pathway explorer20115
NAR Web Server Issue 2011
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tagsenzymes genomics metabolic networks and pathways metagenomics

KaPPA-View4Database Content

http://kpv.kazusa.or.jp/kpv4/ [open in a new window]

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Protein > Databases

KaPPA-View4 is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version. Gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data20119
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals gene expression profiling gene regulatory networks genetic databases humans metabolic networks and pathways metabolome mice rats

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/ [open in a new window]

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Expression > Networks
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

links directory index: 5191
TitlePublication YearGoogle Scholar Citation Count
KEGG for linking genomes to life and the environment20081156
KEGG Atlas mapping for global analysis of metabolic pathways2008146
The KEGG database2002182
KEGG: Kyoto Encyclopedia of Genes and Genomes19993707
NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MADNetTool Content

http://www.bioinfo.hr/madnet [open in a new window]

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Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
MADNet: microarray database network web server20088
NAR Web Server Issue 2008
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tagsgene expression profiling genetic databases metabolic networks and pathways oligonucleotide array sequence analysis signal transduction systems integration

MassTRIXTool Content

http://masstrix.org [open in a new window]

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Other Molecules > Metabolites
Protein > Proteomics

With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
MassTRIX: mass translator into pathways200849
NAR Web Server Issue 2008
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tagsgene expression mass spectrometry metabolic networks and pathways

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