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2D-PAGE -- Proteome database system for microbial and other model organisms research
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| Retrieve descriptive information about the bacterial and other model organisms' proteins identified on 2-D PAGE maps.
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BRIGEP — the BRIDGE-based genome–transcriptome–proteome browser
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| Process and analyze bacterial genome, transcriptome and proteome data. |
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Biodefense Proteomics Resource Center
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| Discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens.
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Bioverse -- functional, structural and contextual annotation of proteins and proteomes
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| Perform protein and proteome annotations. |
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DAnTE -- Data Analysis Tool Extension
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| A statistical tool for quantitative analysis of -omics data.
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DB-PABP -- a Database of Polyanion Binding Proteins
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| Discover interactions between polyanions (PAs) and polyanion binding proteins (PABPs).
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DynaProt 2D -- an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels
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| Search for information on proteomes and two-dimensional (2D) gels.
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EXPASY Proteome Tools Collection
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| Use a collection of tools for protein analyses.
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Entrez Protein
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| Retrieve protein information from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
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GDAP -- A Web Tool for Genome-wide Protein Disulfide Bond Prediction
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| Predict protein disulfide bonds in protein sequences. |
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GELBANK -- A Database of Annotated Two-dimensional Gel Electrophoresis Patterns of Biological Systems with Completed Genomes
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| Search for two-dimensional gel electrophoresis (2DE) gel patterns of proteomes from organisms with known genome information.
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GenProtEC -- Database of Functional Analysis of Escherichia coli K-12 Proteins
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| Characterize functions of unknown Escherichia coli K-12 proteins. |
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Human 2-D PAGE Databases and Proteome Analyses in Health and Disease
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| Search 2D-PAGE data of proteins identified on various reference images.
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IPI International Protein Index
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| Search for comprehensive protein index of human, mouse, and other higher eukaryotic organisms.
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ISPIDER Central -- an integrated database web-server for proteomics
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| Search one or more of the common proteomic databases for specific proteins and/or peptides and to contrast and compare the results.
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InBase -- The New England Biolabs Intein Database
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| Search for sequences and other information of self-catalytic protein splicing elements inteins.
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Integr8 and Genome Reviews -- integrated views of complete genomes and proteomes
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| Explore the biology of organisms with completely deciphered genomes and proteomes. |
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JVirGel -- calculation of virtual two-dimensional protein gels
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| Simulate and analyze proteomics data using virtual two-dimensional (2D) protein gels.
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KOG - Eukaryotic Orthologous Groups of proteins
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| Search Clusters of Orthologous Groups of protein (COGs) for seven (nearly) complete eukaryotic genomes.
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MAPU -- Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
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| Search for information on organellar, cellular, tissue and body fluid proteomes generated by mass spectrometry based proteomics technology.
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MITOPRED -- A Web Server for the Prediction of Mitochondrial Proteins
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| Predict nucleus-encoded mitochondrial proteins in all eukaryotic species.
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NegProt -- Negative Proteome: A tool for comparison of complete proteomes
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| Conduct proteome comparisons.
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OMSSA -- Open mass spectrometry search algorithm
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| Search large MS/MS datasets. |
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Open Proteomics Database
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| Search for mass spectrometry based proteomics data of various model organisms.
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PEP -- Predictions for Entire Proteomes
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| Predict entire proteomes based on available genomes.
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PIR -- The Protein Information Resource
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| Search for integrated and annotated information of proteins.
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POINT -- a database for the prediction of protein-protein interactions based on the orthologous interactome
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| Predict human protein-protein interactome based on interactome databasets of other model organisms. |
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PRIDE -- the PRoteomics IDEntifications database
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| Search for experimentally identified protein and peptides.
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PepSeeker -- a database of proteome peptide identifications for investigating fragmentation patterns
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| Search for peptide identification and ion information from proteome experiments.
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Peptide Finder -- Mapping measured molecular masses to peptides and proteins
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| A web application that facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used.
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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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Predictome -- a database of putative functional links between proteins
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| Predict and visualize functional associations among genes and proteins in many different organisms.
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ProMoST (Protein Modification Screening Tool) -- A web-based tool for mapping protein modifications on two-dimensional gels
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| Calculate the effect of single or multiple posttranslational modifications (PTMs) on protein isoelectric point (pI) and molecular weight and displays the calculated patterns as two-dimensional (2D) gel images.
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Proteome Analyst -- A Web-based Tool for High-throughput Proteome Annotations
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| Predict various properties of each protein in an entire proteome.
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SWISS-2DPAGE Two-dimensional polyacrylamide gel electrophoresis database
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| Search for data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.
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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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Seattle Proteome Center (SPC) - Proteomics Tools
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| Use various software tools to conduct proteomics research.
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SynDB -- Synaptic protein database
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| Search for comprehensive information on known or predicted to be related to the synapse* or synaptic activity.
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The Multi-Q web server for multiplexed protein quantitation
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| Perform large-scale multiplexed protein quantitation based on the iTRAQ labeling method.
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The PeptideAtlas project
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| Search for information on peptides identified in a large set of tandem mass spectrometry proteomics experiments from various organisms.
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The Proteome Analysis database -- A tool for the in silico analysis of whole proteomes
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| Conduct comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes.
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The RESID Database of Protein Modifications
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| Search annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
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The UCSC Proteome Browser
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| Search for a wealth of protein information presented in graphical images and with links to other protein-related Internet sites.
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WILMA -- A genome and proteome annotation system
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| Search for genomes of nematode C.elegans, Homo sapiens, Mus musculus, Arabidopsis thaliana, all annotated by WILMA annotation system. |
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dbPTM -- an information repository of protein post-translational modification
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| Search for information on protein post-translational modifications (PTMs).
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eSLDB -- eukaryotic subcellular localization database
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| Search for annotated information on subcellular localization of eukaryotic proteomes. |
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