> > Interactions, Pathways, Enzymes

Interactions, Pathways, Enzymes

These links include databases for enzyme, metabolic and proteomic pathways. Many of these resources contain dynamic pathway diagrams.

RSS FeedCompact ViewList as XMLList as JSON

Found 124 links

Displaying 15 links

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins tertiary protein structure

ANCHORTool Content

http://structure.pitt.edu/anchor

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

ANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbinding sites drug discovery multiprotein complexes protein databases protein interaction mapping

APIDTool Content

http://bioinfow.dep.usal.es/apid/

Protein > Interactions, Pathways, Enzymes

Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPRD, DIP, IntAct, and MINT.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscomputational biology protein databases protein interaction mapping

ArrayXPathTool Content

http://www.snubi.org/software/ArrayXPath/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.

NAR Web Server Issue 2004NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscluster analysis gene expression profiling genetic databases genetic predisposition to disease medical subject headings oligonucleotide array sequence analysis signal transduction statistical data interpretation systems integration

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

BIND - The Biomolecular Interaction Network DatabaseDatabase Content

http://bond.unleashedinformatics.com/Action

Protein > Interactions, Pathways, Enzymes

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid sequence animals dna factual databases humans macromolecular substances molecular biology protein databases protein interaction mapping proteins rna sequence alignment statistical models tertiary protein structure

BIOBASE Gene Regulation databasesDatabase Content

http://www.gene-regulation.com/pub/databases.html

Protein > Interactions, Pathways, Enzymes

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals binding sites chromatin chromosomes database management systems developmental gene expression regulation dna-binding proteins eukaryotic cells forecasting gene expression profiling gene expression regulation genetic databases genetic promoter regions genetic transcription humans macromolecular substances mice nuclear matrix nuclear proteins nucleic acid databases oligonucleotide array sequence analysis protein databases saccharomyces signal transduction systems integration tissue distribution transcription factors

BioCartaTool Content

http://www.biocarta.com/

Protein > Interactions, Pathways, Enzymes

Information about gene function, proteomic pathways, and reagent exchange; very clear pathway diagrams; can search for pathways by title or browse an organized list.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

BioCyc Knowledge LibraryDatabase Content

http://www.biocyc.org/

Protein > Interactions, Pathways, Enzymes

BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms)

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbacterial gene expression regulation bacterial genome database management systems enzymes escherichia coli escherichia coli proteins genetic databases genome humans metabolism protein databases protein transport signal transduction

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbiological models computer simulation gene expression profiling genetic databases genomics oligonucleotide array sequence analysis protein databases protein interaction mapping saccharomyces cerevisiae proteins signal transduction systems biology systems integration

BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

NAR Web Server Issue 2009
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbiology genetic databases
setsBioMart Ontario Institute for Cancer Research (OICR)

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

BRENDA - The Comprehensive Enzyme Information SystemDatabase Content

http://www.brenda-enzymes.org/

Protein > Interactions, Pathways, Enzymes

Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals enzymes factual databases genomics humans ligands membrane proteins organ specificity protein conformation protein databases protein transport rats substrate specificity systems integration terminology as topic

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

Tags associated with subcategory 'Protein/Interactions, Pathways, Enzymes'

humans computational biology animals protein interaction mapping proteins protein databases algorithms protein sequence analysis genetic databases factual databases binding sites signal transduction systems integration genomics biological models gene expression profiling protein binding amino acid sequence database management systems molecular models tertiary protein structure protein conformation mice sequence alignment genome oligonucleotide array sequence analysis amino acid sequence homology computer simulation ligands dna dictyostelium dna mutational analysis helminth proteins genetic epistasis inborn genetic diseases expert systems helminth genes knowledge drosophila cell cycle substrate specificity fungal genes missense mutation genetic transcription markov chains gene regulatory networks larva saccharomyces dermatan sulfate cultured cells chromatography fibroblasts glucuronates heparin lyase glycosaminoglycans glucuronic acid chondroitin lyases two-hybrid system techniques research neural networks (computer) mutation single-blind method saccharomyces cerevisiae tissue distribution statistical models three-dimensional imaging saccharomyces cerevisiae proteins nuclear matrix nuclear proteins glutamate-trna ligase documentation artificial intelligence gtp-binding proteins monte carlo method polymerase chain reaction statistics as topic ribosomal proteins transcriptional regulatory elements protozoan genome mycobacterium tuberculosis terminology as topic up-regulation nucleic acid regulatory sequences operon plasmodium falciparum eimeria tenella serine endopeptidases regulon yeasts dna fingerprinting heparitin sulfate static electricity hydrophobic and hydrophilic interactions developmental gene expression regulation dna-binding proteins hippocampus forecasting eukaryotic cells t-lymphocyte epitopes predictive value of tests probability