>
Tag
> Links tagged with 'amino acid motifs'

Links tagged with 'amino acid motifs'

RSS FeedCompact ViewList as XMLList as JSON

Found 59 links

Displaying 15 links

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

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.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

3MatrixTool Content

http://motif.stanford.edu/distributions/3matrix/

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

3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.

This content is being maintained by brutlag.

NAR Web Server Issue 2003
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs amino acids animals conserved sequence molecular models protein conformation protein databases proteins sequence alignment

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/

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.

NAR Web Server Issue 2003
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

AlgPredTool Content

http://www.imtech.res.in/raghava/algpred/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.

This content is being maintained by raghavagps.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

DNA > Gene Prediction
Model Organisms > Microbes

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

BAGEL2Tool Content

http://bagel2.molgenrug.nl

DNA > Gene Prediction
Model Organisms > Microbes

BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs anti-bacterial agents bacterial genome bacteriocins data mining genomics open reading frames

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/

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

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs molecular models molecular structure proteins

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

NAR Web Server Issue 2007NAR Web Server Issue 2009
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

CSpritzTool Content

http://protein.bio.unipd.it/cspritz/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

This content is being maintained by silvio.tosatto@unipd.it.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs molecular sequence annotation protein conformation protein structural homology secondary protein structure

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

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

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

eggNOGDatabase Content

http://eggnog.embl.de/version_2/

Protein > Databases

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).s (built from 2,590,259 proteins) and provides a broad functional description for at least 1,966,709 (88%) of them.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs animals archaea bacterial genome computational biology fishes genetic databases humans nucleic acid databases primates protein databases rats tertiary protein structure

FatiGOplusTool Content

http://www.fatigo.org/

DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid motifs animals artificial intelligence binding sites chromosome mapping computational biology dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny programming languages rats sequence alignment systems biology systems integration transcription factors

FF - Fragment FinderTool Content

http://cluster.physics.iisc.ernet.in/ff/

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

FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid motifs molecular structure proteins