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Metabolites

Tools and resources for the analysis of metabolites

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Found 17 links

Displaying 15 links

ARISTOTool Content

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

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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.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry.20111
NAR Web Server Issue 2011
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tagsmass spectrometry small molecule libraries

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

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

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

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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external linksLink on Wikipedia
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

LIPID MAPSTool Content

http://www.lipidmaps.org/tools/index.html [open in a new window]

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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.

links directory index: 535
TitlePublication YearGoogle Scholar Citation Count
LMSD: LIPID MAPS structure database200796
LIPID MAPS online tools for lipid research200760
LMPD: LIPID MAPS proteome database200628
A comprehensive classification system for lipids2005351
NAR Web Server Issue 2007
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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

MetaboAnalyst 2.0Tool Content

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

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and 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. New features for data filtering, editing & normalization

This content is being maintained by Jeff Xia.

links directory index: 75
TitlePublication YearGoogle Scholar Citation Count
MetaboAnalyst: a web server for metabolomic data analysis and interpretation200975
NAR Web Server Issue 2009NAR Web Server Issue 2012
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tagsbiomolecular nuclear magnetic resonance cluster analysis internet mass spectrometry metabolomics software user-computer interface

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/ [open in a new window]

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

links directory index: 127
TitlePublication YearGoogle Scholar Citation Count
MetaPath Online: a web server implementation of the network expansion algorithm200722
Evolutionary changes of metabolic networks and their biosynthetic capacities200614
Hierarchy of metabolic compounds based on their synthesising capacity20069
Expanding metabolic networks: scopes of compounds, robustness, and evolution200582
A cross species comparison of metabolic network functions.20050
Structural analysis of expanding metabolic networks.20040
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 [open in a new window]

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

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks201014
NAR Web Server Issue 2010
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MMMDBDatabase Content

http://mmmdb.iab.keio.ac.jp/ [open in a new window]

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Model Organisms > Databases
Model Organisms > Mouse and Rat
Other Molecules > Metabolites

Mouse Multiple Tissue Metabolome Database: metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
MMMDB: Mouse Multiple Tissue Metabolome Database.20122
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MSEATool Content

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

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

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data201023
NAR Web Server Issue 2010
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tagsanimals dictionaries as topic factual databases humans mammals metabolomics

PlantMetabolomicsDatabase Content

http://plantmetabolomics.vrac.iastate.edu/ver2/ [open in a new window]

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Model Organisms > Plants
Other Molecules > Metabolites

An NSF-funded multi-institutional project developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics--database and tools update.20121
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PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/ [open in a new window]

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

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.

links directory index: 171
TitlePublication YearGoogle Scholar Citation Count
PubChem: a public information system for analyzing bioactivities of small molecules2009171
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/ [open in a new window]

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Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Networks & Interactions, Pathways and 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.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses20104
NAR Web Server Issue 2010
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