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Links tagged with 'substrate specificity'

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Found 18 links

Displaying 15 links

antiSMASHTool Content

http://antismash.secondarymetabolites.org

DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

NAR Web Server Issue 2011
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tagsbacteria bacterial genes bacterial genome biosynthetic pathways fungal genes fungal genome fungi genomics molecular sequence annotation peptide synthases polyketide synthases substrate specificity

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

GPSTool Content

http://csbl.bmb.uga.edu/~ffzhou/gps_web/

Protein > Domains and Motifs

Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.

This content is being maintained by ffzhou.

NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence homology animals binding sites conserved sequence microfilament proteins nerve tissue proteins phosphoproteins phosphorylation protein binding protein kinases protein sequence analysis protein-serine-threonine kinases rats sequence alignment substrate specificity

Human Protein Reference DatabaseDatabase Content

http://www.hprd.org/

Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.

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tagsbrca1 protein computational biology controlled vocabulary disease genomics humans macromolecular substances medical genetics post-translational protein processing protein binding protein databases protein interaction mapping proteins proteome proteomics quaternary protein structure substrate specificity tertiary protein structure

iSPOTTool Content

http://cbm.bio.uniroma2.it/ispot/

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence animals binding sites computational biology factual databases humans ligands molecular models molecular sequence data multigene family peptide fragments peptide library probability protein binding protein databases protein sequence analysis proteins sequence alignment src homology domains substrate specificity tertiary protein structure

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

NEBcutterTool Content

http://tools.neb.com/NEBcutter/index.php3

DNA > Tools For the Bench

NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.

NAR Web Server Issue 2003
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tagsdna methylation dna restriction enzymes dna sequence analysis plasmids restriction mapping substrate specificity type ii site-specific deoxyribonucleases

NetOGlyc Prediction ServerTool Content

http://www.cbs.dtu.dk/services/NetOGlyc/

Other Molecules > Carbohydrates
Protein > Domains and Motifs

Predicts mucin type GalNAc O-glycosylation sites in mammalian proteins.

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tagsalgorithms amino acid sequence animals binding sites carbohydrate conformation factual databases glycoproteins glycosylation hiv envelope protein gp120 humans information systems mammals membrane glycoproteins molecular sequence data mucins n-acetylgalactosaminyltransferases n-acetylglucosaminyltransferases neural networks (computer) protein conformation reproducibility of results secondary protein structure serine substrate specificity threonine viral envelope proteins

NetPhosTool Content

http://www.cbs.dtu.dk/services/NetPhos/

Protein > Sequence Features

NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences

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tagsamino acid motifs amino acid sequence animals binding sites consensus sequence eukaryotic cells glycosylation molecular models neural networks (computer) nuclear proteins phosphoproteins phosphorylation phylogeny reproducibility of results sensitivity and specificity serine substrate specificity tertiary protein structure threonine trans-activators tyrosine

NRPS-PKSTool Content

http://www.nii.res.in/nrps-pks.html

Protein > Domains and Motifs

NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.

NAR Web Server Issue 2004
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tagsmultienzyme complexes peptide synthases protein databases substrate specificity tertiary protein structure

PredikinTool Content

http://predikin.biosci.uq.edu.au

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation

NAR Web Server Issue 2008
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tagsamino acid sequence animals binding sites catalytic domain mice peptides phosphorylation protein databases protein kinases protein sequence analysis protein-serine-threonine kinases substrate specificity

REBASEDatabase Content

http://rebase.neb.com/rebase/rebase.html

Protein > Databases

REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included.

NAR Database Issue 2010
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tagsarchaeal genome bacterial genome binding sites computational biology dna modification methylases dna restriction enzymes genetic databases genomics protein databases substrate specificity tertiary protein structure

SBSPKSTool Content

http://www.nii.ac.in/sbspks.html

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

SBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting residues in docking, and NRPS-PKS for identification of catalytic domains.

NAR Web Server Issue 2010
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tagscatalytic domain molecular models polyketide synthases protein sequence analysis substrate specificity

ScansiteTool Content

http://scansite.mit.edu/

Protein > Domains and Motifs

Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.

NAR Web Server Issue 2003
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tagsalgorithms amino acid motifs amino acid sequence animals binding sites cattle cdc2 protein kinase cdc2-cdc28 kinases computational biology consensus sequence cyclic amp-dependent protein kinases cyclin-dependent kinase 2 cyclin-dependent kinases factual databases fungal proteins genome humans mice mitogen-activated protein kinase kinases molecular models molecular sequence data molecular structure peptides phosphorylation protein binding protein conformation protein databases protein interaction mapping protein kinases protein sequence analysis protein-serine-threonine kinases proteins proteome rats saccharomyces cerevisiae proteins serine signal transduction substrate specificity tertiary protein structure threonine tyrosine

SEARCHGTrTool Content

http://www.nii.res.in/searchgtr.html

Other Molecules > Carbohydrates
Protein > Domains and Motifs

SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs.

NAR Web Server Issue 2005
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tagsanti-bacterial agents binding sites computational biology glycosylation glycosyltransferases metabolism protein conformation protein sequence analysis substrate specificity