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Links tagged with 'enzymes'

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Found 19 links

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3D-FunTool Content

http://3dfun.bioinfo.pl

Protein > 3-D Structure Comparison
Protein > Annotation and Function

3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

NAR Web Server Issue 2008
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tagsalgorithms enzymes molecular models protein structural homology

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)

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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

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

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.

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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

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

E1DSTool Content

http://e1ds.ee.ncku.edu.tw/

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.

NAR Web Server Issue 2008
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tagsamino acid sequence catalytic domain conserved sequence enzymes protein sequence analysis

ENZYME - Enzyme nomenclature databaseDatabase Content

http://us.expasy.org/enzyme/

Protein > Interactions, Pathways, Enzymes

Repository of enzyme nomenclature information; useful selection of cross references to other databases; free for research purposes only.

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tagsenzymes factual databases terminology as topic

ExPASy Molecular Biology ServerResource Content

http://www.expasy.org/

Education > Directories and Portals
Protein > Do-it-all Tools for Protein

Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.

NAR Web Server Issue 2003
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tagsenzymes gel electrophoresis molecular models protein conformation protein databases protein sequence analysis proteins proteomics systems integration

IC50-to-KiTool Content

http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Biochemical Features

A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.

This content is being maintained by flebeda.

NAR Web Server Issue 2009
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tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

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

metaSHARKTool Content

http://bioinformatics.leeds.ac.uk/shark/

Protein > Interactions, Pathways, Enzymes

Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.

NAR Web Server Issue 2006
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tagsanimals biological models coenzyme a dna sequence analysis eimeria tenella enzymes gene expression profiling genomics metabolism plasmodium falciparum protozoan genome

ModellerTool Content

http://salilab.org/modeller/

Protein > 3-D Structure Prediction

Homology or comparative modeling of 3D protein structures.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins biological models carrier proteins computer simulation enzymes factual databases genetic models genome genomics humans kallikreins l-lactate dehydrogenase mathematics molecular models molecular sequence data pancreatic elastase probability protein conformation protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure theoretical models thermodynamics tissue kallikreins trichomonas vaginalis trypsin

PathExpressTool Content

http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/

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

PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.

This content is being maintained by ngoffard.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsalgorithms animals biological models computational biology database management systems enzymes gene expression profiling humans medicago truncatula metabolic networks and pathways metabolism oligonucleotide array sequence analysis protein interaction mapping

PathPredTool Content

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

Protein > Interactions, Pathways, Enzymes

PathPred is an enzyme catalyzed metabolic pathway prediction server. Beginning with a query compound and chemical logic of enzymatic reactions (chemical structure transformation patterns of small molecules), biodegradation pathways of environmental compounds and biosynthesis pathways of secondary metabolites are predicted.

NAR Web Server Issue 2010
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tagsbiocatalysis biosynthetic pathways environmental pollutants enzymes metabolic networks and pathways

ProFuncTool Content

http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/

Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.

NAR Web Server Issue 2005
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tagsbinding sites dna-binding proteins enzymes molecular models protein conformation protein sequence analysis proteins