Proteomics Weblinks

Features

BIND is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature.

BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Clustal W is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

Compute pI/Mw is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot and/or TrEMBL entries or for a user entered sequence.

The Catalytic Site Atlas (CSA) is a resource of catalytic sites and residues identified in enzymes using structural data.

The Dali server is a network service for comparing protein structures in 3D.

The Entrez CDD can be searched to identify proteins that share a conserved interaction domain. It features a collection of multiple sequence alignments for ancient domains and full-length proteins.

Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available.

The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

A curated database of 22,000 monclonal antibody products, hundreds of thousands of product information pages submitted by reagent providers, millions of webpages selected from all 700 reagent suppliers and over 200,000 bioscience-related websites. Antibodies are organized according to genes, species, reagent types (antibodies, phospho-specific antibodies, recombinant proteins, ELISA, siRNA, etc.), patents, and researchers.

The Gene Ontology (GO) Consortium is an international collaboration among scientists at various biological databases, with an Editorial Office based at the EBI. GOA is a project that aims to provide assignments of gene products to the Gene Ontology (GO) resource. The objective of GO is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them.

The GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI) and is a central dataset for other major multi-species databases; such as Ensembl and NCBI.

HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.

The HPR atlas has been created to show the expression and localization of proteins in a large variety of normal human tissues and cancer cells. The data is presented as high resolution images representing immunohistochemically stained tissue sections. Available proteins (genes) can be reached through a specific search (by gene/protein name/id or classification, such as kinase or protease) or by browsing the individual chromosomes.

HPRD represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.

The human protein atlas displays expression and localization of proteins in a large variety of normal human tissues and cancer cells. The data is publically available and presented as high resolution images of immunohistochemically stained tissues and cell lines with over 1500 antibodies and over 1.2 million images.

HumanPRENbase is a derivate of PRENbase with focus on human prenylated proteins. In PRENbase, paralogous proteins are clustered together in their respective larger family when they are highly similar to each other. A scheme of reciprocal BLASTs were employed in order to identify the true orthologues of a set of prenylated human proteins. 238 individual human proteins and their orthologues form the clusters in HumanPRENbase.

IntAct is a protein interaction database and analysis system. It provides a query interface and modules to analyse interaction data.

The Integrated relational Enzyme database (IntEnz) contains enzyme data approved by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.

InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

The iProClass is an integrated resource that provides comprehensive family relationships and structural/functional features of proteins.

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MINT is a relational database designed to store interactions between biological molecules. MINT focuses on experimentally verified protein interactions with special emphasis on proteomes from mammalian organisms.

The Ontology Lookup Service is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format.

PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees. PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.

PDB contains the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.

PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.

Pfam is a large collection of over 8000 multiple sequence alignments and hidden Markov models covering many common protein domains and families. Each family in Pfam can be examined for multiple alignments, protein domain architectures and structures and species distribution.

PHOSIDA (PHOsphorylation SIte Database) allows retrieval of phosphorylation data of any protein of interest. It lists phosphorylation sites associated with particular projects and proteomes or, alternatively, displays phosphorylation sites found for any protein or protein group of interest.

The Phospho.ELM database contains a collection of experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins. The entries, manually annotated and based on scientific literature, provide information about the phosphorylated proteins and the exact position of known phosphorylated instances.

PhosphoSite contains a very comprehensive list of many of the known human and mouse protein phosphorylation sites with very extensive supporting information.

The Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. PIR has made many protein databases and analysis tools freely accessible to the scientific community.

The PMD covers over 81,000 natural as well as artificial mutants of proteins, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, not on proteins. That is, each entry in the database corresponds to one article which may describe one, several or a number of protein mutants.

PRENbase is an annotated database of known and predicted prenylated proteins. Homologous proteins are merged into clusters. This search interface is designed to allow sophisticated queries for the experimental status of the modification (known/predicted...), exclusive or shared types of modifying enzymes (FT, GGT1, GGT2) as well as for evolutionary conservation by constraining the taxonomic distribution within these clusters or for single sequences.

The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data. It has been developed to provide the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications. PRIDE is able to capture details of post-translational modifications coordinated relative to the peptides in which they have been found.

identify the likely biochemical function of a protein from its three-dimensional structure.

Prosite is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. Users can enter a protein sequence or find out the characteristic motifs of domains.

Scansite searches 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.

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa

Swiss 2D-PAGE contains data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps. Proteins can be located on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from Swiss-Prot.

SwissProt is a curated protein sequence database provided by the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB). It strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.

TIGRFAMs are protein families based on Hidden Markov Models or HMMs. Use this page to see the curated seed alignmet for each TIGRFAM, the full alignment of all family members and the cutoff scores for inclusion in each of the TIGRFAMs. Also use this page to search through the TIGRFAMs and HMMs for text in the TIGRFAMs Text Search or search for specific sequences in the TIGRFAMs Sequence Search.

“A Protein Primer” makes music from protein sequences by assigning increasing pitch to amino acids by their increasing hydrophobicity values and the duration of each note is set by the number of codons coding for it.

The UniProt (Universal Protein Resource) for protein sequences and is the central hub for the collection of functional information on proteins, with accurate, consistent, and rich annotation, the amino acid sequence, protein name or description, taxonomic data and citation information. It is a central repository of protein sequence and function created by joining the information contained in UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and PIR.