> Tag > Links tagged with 'protein sequence analysis'

Links tagged with 'protein sequence analysis'

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Found 226 links

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GPCRsclassTool Content

http://www.imtech.res.in/raghava/gpcrsclass/ [open in a new window]

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Protein > Annotation and Function
Protein > Localization and Targeting

GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.

This content is being maintained by raghavagps.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors200538
NAR Web Server Issue 2005
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tagsadrenergic receptors artificial intelligence biogenic amine receptors cholinergic receptors dipeptides dopamine receptors g-protein-coupled receptors protein sequence analysis serotonin receptors

GPSTool Content

http://csbl.bmb.uga.edu/~ffzhou/gps_web/ [open in a new window]

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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.

links directory index: 190
TitlePublication YearGoogle Scholar Citation Count
GPS: a comprehensive www server for phosphorylation sites prediction2005109
GPS: a novel group-based phosphorylation predicting and scoring method200481
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

GraBCasTool Content

http://www.uniklinikum-saarland.de/einrichtungen/fachrichtungen/humangenetik/sof... [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Domains and Motifs

GraBCas is a tool for predicting granzyme B and caspase cleavage sites.

links directory index: 56
TitlePublication YearGoogle Scholar Citation Count
GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences200556
NAR Web Server Issue 2005
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tagscaspases computational biology granzymes protein sequence analysis serine endopeptidases substrate specificity

GRIFFINTool Content

http://griffin.cbrc.jp/ [open in a new window]

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Protein > Annotation and Function

GRIFFIN (G-protein-Receptor Interacting Feature Finding INstrument) uses a support vector machine and hidden markov model to predict G-protein coupled receptors (GPCRs) and G-protein coupling selectivity.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model200541
NAR Web Server Issue 2005
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tagsartificial intelligence g-protein-coupled receptors heterotrimeric gtp-binding proteins ligands markov chains protein sequence analysis

GUIDANCETool Content

http://guidance.tau.ac.il [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

The GUIDANCE web server assesses alignment confidence scores for the identification of unreliable alignment regions. Users input a set of unaligned sequences; output is a graphic visualization of the alignment with confidence scores at each residue.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
GUIDANCE: a web server for assessing alignment confidence scores201015
NAR Web Server Issue 2010
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tagshuman immunodeficiency virus proteins protein sequence analysis sequence alignment viral regulatory and accessory proteins

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching and Classification

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

links directory index: 539
TitlePublication YearGoogle Scholar Citation Count
The HHpred interactive server for protein homology detection and structure prediction2005539
NAR Web Server Issue 2005
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tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment transcription factors

HMMER Web ServerTool Content

http://hmmer.janelia.org [open in a new window]

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Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching and Classification

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
HMMER web server: interactive sequence similarity searching201124
NAR Web Server Issue 2011
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external linksLink on Twitter Link on Wikipedia
tagsalgorithms computational biology information storage and retrieval internet markov chains protein databases protein sequence analysis sequence alignment software

I-Mutant2.0Tool Content

http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure2005164
NAR Web Server Issue 2005
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tagsartificial intelligence point mutation protein engineering protein sequence analysis proteins tertiary protein structure thermodynamics

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

links directory index: 714
TitlePublication YearGoogle Scholar Citation Count
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update20044
The web server of IBM's Bioinformatics and Pattern Discovery group20039
Dictionary-driven prokaryotic gene finding200241
Dictionary-driven protein annotation200237
The emergence of pattern discovery techniques in computational biology200092
Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes.19990
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm1998531
NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

iMOTTool Content

http://caps.ncbs.res.in/imot/iMOTserver.html [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
iMOT: an interactive package for the selection of spatially interacting motifs200410
NAR Web Server Issue 2004
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tagsamino acid motifs amino acid sequence homology protein databases protein folding protein sequence analysis protein tyrosine phosphatases

Institute of Enzymology ServersTool Content

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004
TitlePublication YearGoogle Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates200546
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content2005392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins2005235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes200552
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank2005138
Transmembrane proteins in the Protein Data Bank: identification and classification2004138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation200443
SCide: identification of stabilization centers in proteins.20030
Servers for sequence-structure relationship analysis and prediction20035
On filtering false positive transmembrane protein predictions200257
The HMMTOP transmembrane topology prediction server.20010
Principles governing amino acid composition of integral membrane proteins: application to topology prediction1998795
Stabilization centers in proteins: identification, characterization and predictions1997103
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

InterProDatabase Content

http://www.ebi.ac.uk/interpro/index.html [open in a new window]

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Protein > Domains and Motifs

Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.

links directory index: 3869
TitlePublication YearGoogle Scholar Citation Count
InterPro in 2011: new developments in the family and domain prediction database201211
The InterPro BioMart: federated query and web service access to the InterPro Resource20114
InterPro: the integrative protein signature database2009585
New developments in the InterPro database2007392
InterPro, progress and status in 20052005562
The InterPro Database, 2003 brings increased coverage and new features2003700
InterPro: an integrated documentation resource for protein families, domains and functional sites200299
The InterPro database, an integrated documentation resource for protein families, domains and functional sites2001758
InterPro--an integrated documentation resource for protein families, domains and functional sites2000758
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external linksLink on Wikipedia
tagsalgorithms amino acid repetitive sequences animals computational biology factual databases humans information services metabolic networks and pathways post-translational protein processing protein databases protein sequence analysis proteins search engine sequence alignment systems integration tertiary protein structure

IntFOLDTool Content

http://www.reading.ac.uk/bioinf/IntFOLD/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction20119
NAR Web Server Issue 2011
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tagsbinding sites ligands molecular models protein conformation protein folding protein sequence analysis tertiary protein structure

INTREPIDTool Content

http://phylogenomics.berkeley.edu/intrepid [open in a new window]

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Protein > Annotation and Function
Protein > Sequence Features

The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.

This content is being maintained by kimmen.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis200911
NAR Web Server Issue 2009
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tagsamino acid sequence homology amino acids catalytic domain molecular models phylogeny protein conformation protein sequence analysis proteins

iPBATool Content

http://www.dsimb.inserm.fr/dsimb_tools/ipba/ [open in a new window]

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Protein > 3-D Structure Comparison

iPBA uses specialized protein block substitution matrices and anchor based methodology for pairwise protein structure comparisons.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
iPBA: a tool for protein structure comparison using sequence alignment strategies20113
NAR Web Server Issue 2011
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tagsalgorithms protein conformation protein databases protein sequence analysis sequence alignment

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