> > Domains and Motifs

Domains and Motifs

This section includes links to tools which can give information about protein domains and/or predict motifs, domains, and patterns in peptide sequences.

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Found 116 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
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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

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
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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
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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

AD-ENMTool Content

http://enm.lobos.nih.gov

Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

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
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tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

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
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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

BindNTool Content

http://bioinformatics.ksu.edu/bindn/

Protein > Domains and Motifs
Protein > Sequence Features

BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).

NAR Web Server Issue 2006
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tagsamino acids artificial intelligence binding sites dna dna-binding proteins molecular models protein sequence analysis rna-binding proteins

Blocks WWW ServerTool Content

http://blocks.fhcrc.org/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.

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tagsadenosine triphosphatases algorithms amino acid sequence amino acid sequence homology animals computational biology dna helicases dna-binding proteins factual databases humans molecular sequence data nuclear proteins proteins sequence alignment software design transcription factors

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

CD-SearchDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

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

CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.

NAR Web Server Issue 2004
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tagsamino acid sequence animals consensus sequence conserved sequence molecular models protein databases protein sequence analysis proteins sequence alignment tertiary protein structure time factors

CHOPTool Content

http://www.rostlab.org/services/CHOP/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence homology protein sequence analysis proteomics tertiary protein structure

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

COPSTool Content

http://cops.services.came.sbg.ac.at/

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

The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.

NAR Web Server Issue 2009
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tagsmolecular models protein databases protein folding proteins tertiary protein structure

Tags associated with subcategory 'Protein/Domains and Motifs'

proteins protein sequence analysis protein databases tertiary protein structure computational biology sequence alignment algorithms animals humans amino acid sequence molecular sequence data molecular models amino acid motifs amino acid sequence homology protein conformation binding sites factual databases proteomics structural models protein sorting signals protein tyrosine phosphatases src homology domains triglycerides likelihood functions introns hyperlipidemias hypercholesterolemia ldl lipoproteins male bayes theorem artificial intelligence vldl lipoproteins middle aged automated pattern recognition theoretical models genomics protein folding genome histones initiator codon saccharomyces cerevisiae multigene family leghemoglobin gene expression systems integration archaeal genome archaeal genes anti-infective agents rats biomedical engineering protein structural homology evaluation studies as topic dna chemical dictionaries signal transduction protein-serine-threonine kinases papillomavirus e7 proteins mhc class i genes immunological models peptide fragments t-lymphocyte epitopes aspartic acid endopeptidases polypyrimidine tract-binding protein viral oncogene proteins hla-dr antigens hla-a2 antigen mathematics london fungal genome membrane proteins computer simulation hla-a antigens histocompatibility antigens class i forecasting epitope mapping calmodulin cluster analysis drosophila proteins x-ray crystallography plant dna cattle microfilament proteins protein kinases phosphorylation phosphoproteins nerve tissue proteins serine endopeptidases granzymes hydroxymethylbilane synthase documentation database management systems enzymes molecular structure solvents microtubule-associated proteins porins papain ubiquitin furin membrane glycoproteins mammals