> Tag > Links tagged with 'protein sequence analysis'

Links tagged with 'protein sequence analysis'

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Found 226 links

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(PS)2 Protein Structure Prediction ServerTool Content

http://ps2.life.nctu.edu.tw [open in a new window]

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Protein > 3-D Structure Prediction

(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
(PS)2: protein structure prediction server200627
NAR Web Server Issue 2006
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tagsamino acid sequence consensus sequence molecular models protein conformation protein sequence analysis sequence alignment

3D-JuryTool Content

http://meta.bioinfo.pl/submit_wizard.pl [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

links directory index: 775
TitlePublication YearGoogle Scholar Citation Count
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure2003115
3D-Jury: a simple approach to improve protein structure predictions2003592
Detection of reliable and unexpected protein fold predictions using 3D-Jury200368
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology computer simulation database management systems humans molecular models protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment tertiary protein structure

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

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

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
3D-partner: a web server to infer interacting partners and binding models200727
NAR Web Server Issue 2007
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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

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html [open in a new window]

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

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.

This content is being maintained by brutlag.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database200310
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs200310
NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acids animals conserved sequence database management systems molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment three-dimensional imaging

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/ [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes200914
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

Affymetrix NetAffx Analysis CenterDatabase Content

http://www.affymetrix.com/analysis/index.affx [open in a new window]

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Expression > Transcript Expression Analysis

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

links directory index: 448
TitlePublication YearGoogle Scholar Citation Count
NetAffx: Affymetrix probesets and annotations2003448
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tagsanimals consensus sequence gene expression profiling genetic databases markov chains oligonucleotide array sequence analysis protein sequence analysis proteins

AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
AliasServer: a web server to handle multiple aliases used to refer to proteins200426
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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

Align-mTool Content

http://bioinformatics.vub.ac.be/software/software.html [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
Align-m--a new algorithm for multiple alignment of highly divergent sequences200481
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tagsalgorithms amino acid sequence amino acid sequence homology genetic variation molecular sequence data protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment

AlphaPredTool Content

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

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Protein > 2-D Structure Prediction

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

This content is being maintained by raghavagps.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information200439
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tagsalpha-turns amino acid sequence ANN molecular sequence data neural networks (computer) prediction protein databases protein sequence analysis proteins roc curve secondary protein structure sequence alignment sequence-to-structure network statistical models structure-to-structure network

ALTERTool Content

http://sing.ei.uvigo.es/ALTER/ [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

ALTER is a program-oriented web tool for the conversion between DNA and protein alignments.

This content is being maintained by lipido.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
ALTER: program-oriented conversion of DNA and protein alignments20109
NAR Web Server Issue 2010
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tagsdna sequence analysis protein sequence analysis sequence alignment

ANNIETool Content

http://annie.bii.a-star.edu.sg [open in a new window]

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Protein > Annotation and Function

ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
ANNIE: integrated de novo protein sequence annotation200915
NAR Web Server Issue 2009
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tagsalgorithms protein sequence analysis

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/ [open in a new window]

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Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences200424
NAR Web Server Issue 2004
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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/ [open in a new window]

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Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing20113
NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

BAR-PLUSTool Content

http://bar.biocomp.unibo.it/bar2.0 [open in a new window]

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Protein > Annotation and Function

BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, GO, Pfam and PDB.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.20111
NAR Web Server Issue 2011
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tagscluster analysis molecular sequence annotation protein conformation protein sequence analysis proteins sequence alignment

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