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Links tagged with 'metabolic networks and pathways'

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Found 25 links

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BioMet ToolboxTool Content

http://www.sysbio.se/BioMet

Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Interactions, Pathways, 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.

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

BioPaxResource Content

http://www.biopax.org/

Computer Related > Bio-* Programming Tools

The BioPAX web site provides information about a collaborative effort to create a data exchange format for biological pathways.

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tagscomputational biology information dissemination metabolic networks and pathways programming languages signal transduction

BRENDADatabase Content

http://www.brenda-enzymes.org

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.

NAR Database Issue 2011
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tagsenzymes ligands metabolic networks and pathways protein conformation protein databases

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de

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.

NAR Database Issue 2011
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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

Expression > Networks
Model Organisms > Microbes
Protein > Interactions, Pathways, 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.

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/

Other Molecules > Metabolites
Protein > Interactions, Pathways, 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.

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

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.

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

Other Molecules > Metabolites
Protein > Interactions, Pathways, 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.

NAR Web Server Issue 2011
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tagsgenomics metabolic networks and pathways

Gramene database in 2010Database Content

http://www.gramene.org

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.

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

InterProDatabase Content

http://www.ebi.ac.uk/interpro/index.html

Protein > Domains and Motifs

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

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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

Protein > Interactions, Pathways, Enzymes

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

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/

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.

NAR Database Issue 2011
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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/

Expression > Networks
Protein > Interactions, Pathways, 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.

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

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.

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

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.

NAR Web Server Issue 2008
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tagsgene expression mass spectrometry metabolic networks and pathways