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Links tagged with 'protein kinases'

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@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/

Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

DILIMOTTool Content

http://dilimot.embl.de/

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

Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.

NAR Web Server Issue 2006
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tagsamino acid motifs amino acid sequence animals binding sites genome humans microtubule-associated proteins molecular models molecular sequence data peptides protein binding protein kinases protein sequence analysis protein sorting signals proteins tertiary protein structure

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

KinasePhosTool Content

http://kinasephos.mbc.nctu.edu.tw/

Protein > Domains and Motifs

KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences.

NAR Web Server Issue 2005
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tagscomputational biology markov chains phosphoproteins phosphorylation protein kinases protein sequence analysis

KinasePhos 2.0Tool Content

http://kinasephos2.mbc.nctu.edu.tw/

Protein > Domains and Motifs

KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.

NAR Web Server Issue 2007
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tagscatalytic domain computational biology computer simulation markov chains neural networks (computer) phosphoproteins phosphorylation probability protein kinases protein sequence analysis sensitivity and specificity

KinDOCKTool Content

http://abcis.cbs.cnrs.fr/kindock/

Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).

NAR Web Server Issue 2006
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tagsadenosine triphosphate binding sites drug design ligands protein conformation protein kinase inhibitors protein kinases

P2CSDatabase Content

http://www.p2cs.org

Protein > Databases

P2CS is a database for prokaryotic two-component systems (TCSs). The database annotates and classifies TCS proteins from completely sequenced prokaryotic genomes and metagenomes. TCS complements can be browsed by metagenome, replicon or sequence cluster (and these genesets are available for download by users). A variety of database-wide or taxon-specific searches are also supported. Each TCS protein is fully annotated with sequence-feature information including replicon context, while properties of the predicted proteins can be queried against several external prediction servers to suggest homologues, interaction networks, sub-cellular localization and domain complements. There is also a CGView representation of the distribution of TCS genes around a replicon, categorization of TCS genes based on gene organization, an expanded domain-based classification scheme, a P2CS 'gene cart' and categorization on the basis of sequence clusters.

NAR Database Issue 2011
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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins intercellular signaling peptides and proteins molecular sequence annotation protein databases protein kinases

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

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

RegPhosDatabase Content

http://RegPhos.mbc.nctu.edu.tw

Protein > Databases

RegPhos is a database for exploration of the phosphorylation network associated with an input of genes/proteins. Subcellular localization information is also included.

NAR Database Issue 2011
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tagsgene expression profiling humans insulin receptor substrate proteins phosphoproteins phosphorylation protein databases protein interaction mapping protein kinases signal transduction

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