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Metabolites

Tools and resources for the analysis of metabolites

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Found 14 links

Displaying 14 links

ARISTOTool Content

http://www.ionspectra.org/aristo

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules

Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.

NAR Web Server Issue 2011
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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

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

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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HMDBDatabase Content

http://www.hmdb.ca/

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.

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tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance humans metabolism organ transplantation

LIPID MAPSTool Content

http://www.lipidmaps.org/tools/index.html

Human Genome > Other Resources
Other Molecules > Metabolites

LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.

NAR Web Server Issue 2007
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tagsanimals chemical models computational biology database management systems factual databases glycosphingolipids humans isomerism lipid metabolism lipids mice molecular conformation molecular structure polysaccharides protein databases proteome proteomics terminology as topic

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

MetaboAnalystTool Content

http://www.metaboanalyst.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis.

This content is being maintained by Jeff Xia.

NAR Web Server Issue 2009
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tagsbiomolecular nuclear magnetic resonance cluster analysis mass spectrometry metabolomics

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

NAR Web Server Issue 2007
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tagsadenosine triphosphate algorithms animals archaea bacteria biological evolution biological models cell physiological phenomena chemical models coenzymes computational biology computer simulation energy metabolism eukaryotic cells factual databases gene expression profiling genetic models genetic variation glucose glycolysis humans inorganic chemicals kinetics metabolism molecular evolution nerve net organic chemicals phosphates phylogeny physiological adaptation protein biosynthesis proteins signal transduction species specificity substrate specificity

MetExploreTool Content

http://metexplore.toulouse.inra.fr

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetExplore is a web tool that links metabolites identified in untargeted metabolomics experiments within the context of genome-scale metabolic networks. Metabolomics data is mapped onto the specific metabolic network of an organism in a interactive graphical display.

This content is being maintained by l.cottret.

NAR Web Server Issue 2010
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tagsgenome metabolic networks and pathways metabolomics

MSEATool Content

http://www.msea.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

Metabolite Set Enrichment Analysis (MSEA) performs enrichment analyses for (primarily human) metabolomic studies. It identifies patterns of metabolite concentration changes in a biologically meaningful context. MSEA uses a library of ~6300 predefined metabolite sets from pathways, disease signatures, genetic traits, and cellular/tissue locations. MSEA also facilitates conversion between metabolite common names, synonyms and other database identifies.

This content is being maintained by Jeff Xia.

NAR Web Server Issue 2010
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tagsanimals dictionaries as topic factual databases humans mammals metabolomics

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

NAR Web Server Issue 2009
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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

SIMCOMP/SUBCOMPTool Content

http://www.genome.jp/tools/simcomp/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.

NAR Web Server Issue 2010
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tagsfactual databases isomerism metabolic networks and pathways molecular structure

Yeast MetaboliNERTool Content

http://nactem-t1.mib.man.ac.uk/metaboliner/

Literature > Text Mining and Semantics
Model Organisms > Yeast
Other Molecules > Metabolites

Yeast MetaboliNER is a tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome.

This content is being maintained by pthompson.

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tagsmetabolites named entity recognition text mining yeast

Tags associated with subcategory 'Other Molecules/Metabolites'

factual databases metabolic networks and pathways humans metabolomics molecular structure animals coenzymes energy metabolism computer simulation computational biology eukaryotic cells biological models chemical models protein databases polysaccharides proteome proteomics cell physiological phenomena terminology as topic gene expression profiling molecular conformation phylogeny phosphates physiological adaptation protein biosynthesis species specificity signal transduction proteins organic chemicals nerve net glucose genetic variation genetic models glycolysis inorganic chemicals molecular evolution metabolism kinetics mice substrate specificity ethanol algorithms dictionaries as topic mammals protein interaction mapping genome gene expression regulation biological evolution bacteria named entity recognition metabolites text mining yeast archaea adenosine triphosphate gene expression transcription factors biochemical phenomena mass spectrometry cluster analysis database management systems glycosphingolipids lipids lipid metabolism isomerism plants pharmaceutical preparations biomolecular nuclear magnetic resonance biochemistry organ transplantation national library of medicine (u.s.) united states structure-activity relationship pharmacology