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2Dsweep -- protein annotation by secondary structure elements
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| Perform secondary structure predictions on protein sequences.
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3MOTIF -- a protein structure visualization system for conserved sequence motifs
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| Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.
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AFAWE -- Automatic functional annotation in a distributed Web Services Environment
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| Protein function prediction and annotation in an integrated environment powered by web service.
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Active Sequences Collection (ASC) database -- A new tool to assign functions to protein sequences
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| Search for short active protein sequences with demonstrated biological activities.
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BindN -- a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
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| Predict DNA and RNA binding sites in protein sequences.
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Blocks -- Ungapped segments in conserved protein sequences
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| Search for ungapped segments corresponding to the most highly conserved regions of proteins.
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CASTp -- computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
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| Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. |
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COMe -- The bioinorganic motif database
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| Classify metalloproteins and some other complex bioinorganic proteins using the concept of bioinorganic motif.
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CRP -- Cleavage of Radiolabeled Phosphoproteins
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| Design and interpret experiments to identify protein phosphorylation sites by Edman sequencing of unseparated peptides.
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CSA -- The Catalytic Site Atlas
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| To search for catalytic residue annotation for enzymes in the Protein Data Bank.
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ConSurf-DB -- evolutionary conservation profiles of protein structures database
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| Automatically calculate evolutionary conservation scores of key amino acid residues and map them on protein structures. |
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DILIMOT -- discovery of linear motifs in proteins
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| Predict short linear motifs (3-8 residues) in a set of protein sequences.
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Dasty2 -- an Ajax protein DAS client
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| A web client for visualizing protein sequence feature information using DAS.
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DomainSweep -- protein annotation by domain analysis
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| Identify the domain architecture within a protein sequence.
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E1DS -- catalytic site prediction based on 1D signatures of concurrent conservation
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| Predict enzyme catalytic site.
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ELM server -- a new resource for investigating short functional sites in modular eukaryotic proteins
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| Predict functional sites in eukaryotic proteins.
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EVALLER: a web server for in silico assessment of potential protein allergenicity
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| Predict allergenicity of a protein sequence.
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EXPASY Proteome Tools Collection
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| Use a collection of tools for protein analyses. |
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EXPASY-Findmod
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| Predict potential protein post-translational modifications and find potential single amino acid substitutions in peptides.
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EzCatDB -- the Enzyme Catalytic-mechanism Database
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| Search for information related to the catalytic mechanisms of enzymes. |
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FingerPRINT Scan
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| Identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.
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FireDB -- a database of functionally important residues from proteins of known structure
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| Search for functional annotation of important sites in proteins with known structures.
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HGPD -- Human Gene and Protein Database
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| A database presenting experiment-based results in human proteomics.
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HHsenser -- exhaustive transitive profile search using HMM–HMM comparison
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| Conduct exhaustive intermediate profile searches of a set of homologous protein sequences.
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Integrating protein annotation resources through the Distributed Annotation System
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| Annotate protein using this integrated annotation resource.
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InterProScan -- protein domains identifier
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| Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites. |
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JAFA -- a protein function annotation meta-server
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| Conduct comprehensive protein function annotation.
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KFC -- Knowledge-based FADE and Contacts
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| Interactive forecasting of protein interaction hot spots.
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KinasePhos -- a web tool for identifying protein kinase-specific phosphorylation sites
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| Identify protein kinase-specific phosphorylation sites based on sequences and coupling patterns. |
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MAGIIC-PRO -- detecting functional signatures by efficient discovery of long patterns in protein sequences
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| Discover long patterns in protein sequences.
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MALISAM -- Manual ALIgnments for Structurally Analogous Motifs
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| Database containing pairs of structural analogs and their alignments.
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MEME -- discovering and analyzing DNA and protein sequence motifs
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| Find sequence patterns in DNA and protein sequences.
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MINER -- software for phylogenetic motif identification
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| Identify phylogenetic motifs in protein sequences.
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MODi -- a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra
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| Predict multiple post-translational peptide modifications from tandem mass spectra.
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MassNet -- a functional annotation service for protein mass spectrometry data
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| A web service for analyze and annotate mass spectrometry data.
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MeMo -- a web tool for prediction of protein methylation modifications
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| Predict protein methylation sites.
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Minimotif Miner -- a tool for investigating protein function
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| Find motifs in a protein sequence.
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Motif3D -- Relating protein sequence motifs to 3D structure
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| Visualize protein sequence motifs on the 3D protein structures.
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MotifScan
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| Find presence of any known protein motif (Prosite and Pfam) in a protein sequence.
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NMT -- The MYR Predictor
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| Analyze proteins for the presence of N-terminal N-myristoylation site.
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NetNGlyc -- N-Glycosylation sites prediction tool
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| Find the presence of N-Glycosylation sites in human proteins.
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NetOGly 3.1 -- O-glycosylation sites prediction tool
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| Find the presence of O-GalNAc (mucin type) glycosylation sites in mammalian proteins.
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NetPhos 2.0 -- Phosphorylation sites predictions
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| Analyze eukaryotic proteins for the presence of serine, threonine and tyrosine phosphorylation sites.
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NetPhosK 1.0 Server -- kinase specific eukaryotic protein phosphorylation sites prediction tool
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| Find possible kinase specific phosphorylation sites in eukaryotic proteins.
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NeuroPred -- a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides
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| Predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences.
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O-GLYCBASE
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| Search for information about glycoproteins with O-linked and C-linked glycosylation sites.
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PAR-3D -- Protein Active site Residue - 3D structural motif
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| A server to predict protein active site residues.
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PDBSite -- a database of the 3D structure of protein functional sites
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| Search for structural and functional information on the protein functional sites.
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PDBSiteScan -- A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
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| Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites. |
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PEDANT -- Protein Extraction, Description and ANalysis Tool
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| Conduct genome wide functional and structural analysis. |
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PHOSIDA -- Phosphorylation site database
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| Search for phosphorylation data of any protein of interest.
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PHOSPHORYLATION SITE DATABASE
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| Search for information on prokaryotic proteins that undergo serine, threonine, or tyrosine phosphorylation.
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PPSearch
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| Search your query sequence against PROSITE pattern database for protein motifs.
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PRINTS and its automatic supplement, prePRINTS -- A compendium of protein fingerprints
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| Search for protein fingerprints.
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PROMISE -- The Prosthetic groups and Metal Ions in Protein Active Sites Database
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| Search for comprehensive sequence, structural, functional and bibliographic information on metalloproteins and other complex proteins, with an emphasis on active site structure and function.
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PROSITE
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| Identify protein families and domains for a given protein sequence.
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PatMatch -- a program for finding patterns in peptide and nucleotide sequences
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| Search for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences.
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PepCyber:P~PEP -- a database of human protein protein interactions mediated by phosphoprotein-binding domains
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| Database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions.
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PeptideCutter -- protein cleavage sites prediction tool
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| Predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.
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Phobius -- A combined transmembrane topology and signal peptide predictor
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| Predict combined transmembrane topology and signal peptides.
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Phospho.ELM -- a database of phosphorylation sites
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| Search for eukaryotic phosphorylation sites.
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Phospho3D -- a database of three-dimensional structures of protein phosphorylation sites
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| Search for 3D structure and functional annotation of phosphorylation sites in proteins. |
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PhosphoSite -- A bioinformatics resource dedicated to physiological protein phosphorylation.
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| Search the database of in vivo phosphorylation sites of human and mouse proteins |
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Pratt Protein motif and pattern discovery
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| Find the presence of protein motifs and patterns in an amino acid sequence.
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PrediSi -- Prediction of Signal Peptides and their Cleavage Positions
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| Predict signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences.
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Prediction of lipid posttranslational modifications and localization signals from protein sequences -- big-Pi, NMT and PTS1.
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| Predict lipid posttranslational modifications and localization signals from protein sequences.
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ProFunc -- a server for predicting protein function from 3D structure
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| Predict protein functions based on known structures. |
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ProMateus--an open research approach to protein-binding sites analysis
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| Predict the location of potential protein-protein binding sites for unbound proteins.
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ProTeus -- identifying signatures in protein termini
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| Identify short linear signatures in protein termini.
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ProtSweep -- protein annotation by homology
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| Analyze and identify newly obtained protein sequences.
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Protemot -- prediction of protein binding sites with automatically extracted geometrical templates
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| Predict protein binding sites in a protein sequence based on geometrical analysis of protein tertiary substructures.
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QuasiMotiFinder -- protein annotation by searching for evolutionarily conserved motif-like patterns
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| Search for evolutionarily conserved motif-like patterns in protein sequences.
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RNABindR -- software for prediction of RNA binding residues in proteins
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| Web-based server for analyzing and predicting RNA binding sites in proteins.
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SCANMOT -- searching for similar sequences using a simultaneous scan of multiple sequence motifs
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| Search for similarities between proteins by simultaneous matching of multiple motifs. |
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SDPpred -- A Tool for Prediction of Amino Acid Residues that Determine Differences in Functional Specificity of Homologous Proteins
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| Predict residues in protein sequences that determine the proteins' functional specificity.
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SDR -- Specificity Determining Residues Database
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| Predict specificity-determining residues in protein families.
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SLiMDisc -- Short, Linear Motif Discovery
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| Find shared motifs in proteins with a common attribute.
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STAR -- Predicting recombination sites from amino acid sequence
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| Predict recombination sites from amino acid sequence.
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SUMOsp -- a web server for sumoylation site prediction
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| Conduct in silico sumoylation sites prediction.
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SURFACE -- SUrface Residues and Functions Annotated, Compared and Evaluated
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| Compare annotated protein surface regions and find putative surface functional sites. |
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SWAKK -- a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
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| Detect protein sequence section under positive evolution selection.
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ScanProsite
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| Search for motifs and patterns within protein sequences.
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ScanProsite -- detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
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| Detect patterns, profiles and motifs in a protein sequence.
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ScanSite 2.0 -- Proteome-wide prediction of cell signaling interactions using short sequence motifs
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| Search for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.
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Sequence Motif Search
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| Search the presence of a motif in either amino acid sequence or nucleotide sequence.
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Sequence harmony -- detecting functional specificity from alignments
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| Detect subfamily specific positions from a multiple alignment.
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Signal-3L -- A 3-layer approach for predicting signal peptides
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| Predict signal peptides.
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SignalP -- Machine learning approaches to the prediction of signal peptides, their cleavage sites, and other protein sorting signals
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| Predict signal peptides and their cleavage sites.
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SitesBase -- a database for structure-based protein–ligand binding site comparisons
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| Search for known ligand binding sites of proteins within the PDB.
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SubSeqer -- sequence pattern finder
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| A graph-based approach for the detection and identification of repetitive elements in low-complexity sequences.
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Sulfinator -- tyrosine sulfation sites prediction tool
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| Predict the presence of tyrosine sulfation sites in protein sequences
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SuperSite -- Ligand Binding Site Database
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| Look at protein structure from a ligand and binding site perspective.
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Swiss EMBnet node web server
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| Use a collection of bioinformatics tools at this portal site. |
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TMFunction -- The Functional Database of Membrane Proteins
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| Find information about functional residues in alpha-helical and beta-barrel membrane proteins.
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TOPDOM -- Conservatively Located Domains and Motifs in Transmembrane Proteins
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| Database of domains and motifs with conservative location in transmembrane proteins.
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The EMOTIF database
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| Search for highly conserved and specific protein sequence motifs.
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TreeDet -- Predicting Functional Residues in Protein Sequence Alignments
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| Predict functional sites in protein sequence alignments use different methodologies.
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WebFEATURE -- an interactive web tool for identifying and visualizing functional sites on macromolecular structures
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| Scan query structures for functional sites in both proteins and nucleic acids. |
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WebProAnalyst -- an interactive tool for analysis of quantitative structure–activity relationships in protein families
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| Analyze quantitative structure-activity relationship of related protein families.
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eBLOCKs -- enumerating conserved protein blocks to achieve maximal sensitivity and specificity
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| Search for ungapped alignments of highly conserved regions among a protein family or superfamily.
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firestar -- prediction of functionally important residues using structural templates and alignment reliability
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| An expert system for predicting ligand-binding residues in protein structures.
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iMOTdb -- a comprehensive collection of spatially interacting motifs in proteins
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| Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage. |
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siteFiNDER|3D -- a web-based tool for predicting the location of functional sites in proteins
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| Predict functionally important regions in proteins of known structure.
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