ST NetWatch: Protein Databases

Biological Macromolecule Crystallization Database 

Structures and crystalization conditions for 3547 crystal entries from 2526 biological macromolecules, maintained by the National Institute of Standards and Technology.

(Free Site)

Cytokines Online Pathfinder Encyclopaedia 

The Cytokines Online Pathfinder Encyclopaedia (COPE) is part of a site designed to help users "Cope with Cytokines". Horst Ibelgaufts' site provides basic information on cytokines and their nomenclature through an alphabetized index. The information is actually an electronic, revised, and updated version of the "Dictionary of Cytokines", published in 1995 by VCH Publishers Inc., which is now out of print. There are other resources lurking under the "Browse contents, new entries, subdictionaries" link that include "miniCOPE dictionaries" on apoptosis, chemokines, hematology, metalloproteinases, and virulence factors. There is also a list of cell lines (over 200 of them!) used in cytokine research. The site has received numerous awards and, according to the statistics page, often serves upwards of 40,000 page impressions a week.

(Free Site)

Database of Interacting Proteins 

An interactive database based on the published data regarding protein-protein interactions that allows you to search for protein partners. Sequences can be tested for reported interacting proteins or searches can be performed using a text interface using keywords or citation information. New cross-referencing feature links to ProLinks, a database with more than 10 million linkages in over 80 genomes. The site is free for non-profit, academic use. Updated February 7, 2004, with a more user-friendly interface.

(Free Site)

EF-Hand Calcium-Binding Proteins Data Library 

The EF-Hand Calcium-Binding Proteins Data Library has sections on general, sequence, and structural information, and analytic tools that allow you to find homologs for EF-hand proteins or calculate the per residue solvent accessible surface area for several EF-hand proteins. This site does not appear to actively maintained. However, there is still valuable information for the calcium-binding protein afficianado.

(Free Site)

GPCRDB: Information System for G Protein-Coupled Receptors 

Sequences, alignments, models, mutants, phylogenetic trees, ligand-binding data, and more...a labor of love to delight the true fan of G protein-coupled receptors. The discussion forum provided by Scientist Solutions offers practical advice for wet lab research on these proteins. Viewing the models requires RasMol, but the snake-like diagrams are readily viewable and available for downloading as scalable vector graphic (SVG) or GIF files. This site was updated in 2005.

(Free Site)

Human 2-D PAGE Databases 

Where does 14-3-3 run on a 2D IEF gel of human keratinocytes? Find out here. A beautiful collection of human and mouse IEFs and immunoblots for selected cell types, with thousands of proteins identified and databased. Site was updated in November 2000.

(Free Site)

Human Protein Reference Database (HPRD) 

Under the guidance of Dr. Akhilesh Pandey of Johns Hopkins University and the Institute of Bioinformatics, a group of biologists, bioinformaticists and bioengineers created this site based exclusively on manually curated information. The site offers illustrations and detailed information about proteins, including molecular functions and protein-protein interactions. The query interface offers many different ways to locate a protein in the database, such as based on molecular class, protein domain, structural motifs, chromosomal location, and tissue expression. Users can also suggest a new protein or become a molecule authority. The site includes a tool called PhosphoMotif Finder, which identifies phosphorylation motifs in submitted sequences based on matching those found in the published literature. Academic use of the site is free.

(Free Site)

IUPHAR Receptor Database 

The International Union of Pharmacology (IUPHAR) maintains a searchable database on G protein-coupled receptors (GPCRs), with overviews on receptor families as well as detailed information on the structure, function, tissue distribution, and ligands of individual receptors. A human-centric list that includes potential receptors with seven transmembrane-spanning regions (excluding sensory receptors and pseudogenes) as well as known GPCRs is also available.

(Free Site)

kinase.com 

The site "kinase.com" is devoted to the “genomics, evolution and function of protein kinases.” It is maintained by Gerard Manning’s lab at the Salk Institute, the same group that generated the Human Kinome Poster. The site includes KinBase, a multi-species kinase database. KinBase searches can be restricted by name, component protein domain, family-subfamily classification, or species. Pages for individual kinases include chromosome map position, if known, links to information about that protein at iHOP, PhosphoSite, and Gene Cards, as well as sequence data at Entrez Gene. kinase.com includes links to ongoing kinome projects in various species and provides a free phylogenetic tree navigation tool called HyperTree. The homepage and “What’s New” section have summaries of recent relevant research as well as news about the site and updates to KinBase or kinome projects.

(Free Site)

Kinomer 

Kinomer is a multispecies library of protein kinases classified into groups based on sequence and functional similarities. Kinases are divided into eight conventional and four atypical protein kinase groups; descriptions of each group are available on the site. The library includes kinases from various organisms: 16 fungi, 7 mammals, 6 plants, 4 fish, 4 insects, 3 protozoa, chicken, sea squirt, and more. Users can search the database to identify specific types of kinases in a single species or in multiple species; one can generate, for example, a list of the tyrosine kinases from chicken, the casein kinases from all 16 species of fungi, or every atypical protein kinase in the mouse. Jalview, a Java sequence alignment editor applet, allows users to sort, perform alignments, determine consensus sequences, and generate molecular phylogenies with all or a subset of the search results. Users may also upload or paste a protein sequence into a search window to classify a kinase into one of the 12 main groups and compare it to related kinases. This resource was developed by Geoff Barton’s research group at the University of Dundee, and the library is freely available for download.

(Free Site)

Ligand-Gated Ion Channel Database 

Created by Nicolas Le Novère and Jean-Pierre Changeux, the Ligand-Gated Ion Channel Database (LGICdb) contains nucleic acid and protein sequences of subunits of three classes of ligand-gated ion channels: The Cys-Loop Superfamily, the ATP-Gated Channels, and the Glutamate-Activated Cationic Channels. Multiple sequence alignments can be easily generated, and some phylogenetic studies of the superfamilies are provided. The nomenclature is unique, but there is a key to the naming convention. Data can be accessed by searching keywords or sequences or by browsing within each channel superfamily. Custom sequence alignments are very easy to generate, although alignments of complete genes takes a bit of time. LGICdb is a project of the Computational Neurobiology group at EMBL-EBI.

(Free Site)

LOCATE: Subcellular Localization Database 

LOCATE is a database with information about the subcellular localization and membrane topology of proteins from the mouse RIKEN FANTOM3 protein sequences. The information can be accessed through various browsing options and by searching. For example, by simply clicking on a subcellular compartment in the visual representation of a cell, one is provided with a list of proteins that can be further sorted. The database may also be searched and the output is available in multiple formats, including machine-readable options. The high-throughput, computational pipeline MemO was used to predicted membrane organization. The subcellular locations of the proteins were determined by a high-throughput, immunofluorescence-based assay and by manual review of peer-reviewed publications. This database is maintained by the Institute of Molecular Bioscience, The University of Queensland and the ARC Centre in Bioinformatics.

(Free Site)

MINT: The Molecular INTeraction Database 

The MINT database contains curated information about experimentally verified protein-protein interactions, and you can search the database to find your favorite protein’s binding partners. Interaction information obtained from the literature and from high throughput screens includes binary interactions only; information on higher-order complexes is not available. The search engine works best if you use an accession number or specific gene name rather than a family name. You can view your favorite protein’s binding partners as a list, link to the literature that illustrates the interaction, and even download binding partners’ sequence files easily.

(Free Site)

Molecular Class-Specific Information System (MCSIS) 

This collection of information systems has grown from the original GPCRDB (G protein-coupled receptor database) to now include databases for five different types of proteins: The GPCRDB, The NucleaRDB (nuclear receptors), The PrionDB (prion proteins), The KChannelIDB (potassium channels), and the GPCRIPDB (GPCR interacting proteins). Groups in Europe and the US collaborate to create, maintain, and curate these databases and information systems.

(Free Site)

Nuclear Receptor Resource 

The Nuclear Receptor Resource Project allows ready access to a collection of individual databases on various members of the steroid and thyroid hormone family. Individual databases include the Vitamin D Receptor Resource, the Thyroid Receptor Resource, the Steroid Receptor Associated Proteins Resource, the Glucocorticoid Receptor Resource, the Androgen Receptor Mutation Database, the Peroxisome Proliferator Activated Receptor Resource, and the Estrogen Receptor Resource. There is a wealth of information in the component resources, and the Nuclear Receptor Resource Home Page has links to researchers in the field as well as a graphics library. Information on meetings and employment, however, appeared out of date.

(Free Site)

NucleaRDB: Information System for Nuclear Receptors 

Sequences, multiple sequence alignments, phylogenetic trees, and more for nuclear receptors. The database is current and is easy to navigate.

(Free Site)

NURSA: Nuclear Receptor Signaling Atlas 

An information portal for members of the nuclear receptor research community, NURSA seeks to develop an understanding of the structure and function of all nuclear receptors. The site serves as a comprehensive database of all relevant findings in the field, with features that include a detailed, user-friendly animated tutorial, an e-journal, a searchable molecular database with PubMed links, and a library of annotations and resource links. There’s even a calendar of upcoming meetings. Coming soon are personal laboratory pages for researchers, an interactive discussion forum, and a jobs database.

(Free Site)

Orientations of Proteins in Membranes database 

This database, maintained by Andrei Lomize, Mikhail Lomize and Irina Pogozheva of the University of Michigan, provides representations of proteins with respect to the lipid bilayer. A computational method is applied to optimize the representation of proteins with known structures relative to the lipid bilayer. The initial data includes predominantly integral membrane proteins and a some peripheral membrane proteins or peptides that interact with the membrane. The structures are based on data from the Protein Data Bank (PDB). The site can be searched or browsed, and the files are available for downloading. Details about the computational analysis is also provided. Each structure is available as an image oriented with respect to the membrane. One of the neatest features is that each structure has a Chime, Jmol, or Webmol version that allows the orientation from the intracellular and extracellular side as well as packing through the membrane to be readily visible.

(Free Site)

PDSP Drug Database 

The NIMH Psychoactive Drug Screening Program (PSDP) database is a searchable, interactive database of Ki values (affinity constants) for a large number of G-protein coupled receptors (GPCR's), transporters, and ion channels. The database is updated daily and has a feature for user-supplied data. If you are looking for what proteins may bind your test ligand and with what affinity or if you're looking for a ligand to use to identify a receptor, then this database is incredibly useful. Access to the database is free and it is a NIH-sponsored, non-commercial site.

(Free Site)

Pfam 

Pfam is a database of protein domain families that can be used to identify domains in a protein of interest and to learn more about the structure, function, and evolution of those domains. The protein domain families in the database are divided into two categories, Pfam-A and Pfam-B, which differ in the quality of their sequence alignments. Pfam-A families are small groups built from manually curated short alignments, which are expanded to full alignments by an automated process. Pfam-B families are generated by an entirely automated process and represent a larger set of alignments. Together, these two datasets confer both reliability and comprehensiveness to the database. The database may be searched by query sequence, accession number, PDB identifier, family name, or keyword. Each family’s entry includes extensive information about the sequence, structural and functional characteristics, and variations among family members. Information about the domain organization of family members, the distribution of family members across different species, and documented protein-protein interactions is also available. Phylogenetic trees illustrate the relatedness of different family members, and interactive JMOL images allow the user to examine structures of the proteins from any angle.

(Free Site)

PHOSIDA: Phosphorylation Site Database 

PHOSIDA is a library of phosphorylation and acetylation sites determined by mass spectrometry analysis in Matthias Mann's laboratory at the Max Planck Institute for Biochemistry. The database includes protein phosphorylation sites from mouse, human, fly, nematode, yeast, and several species of bacteria, and human protein acetylation data. Each species-specific dataset may be searched by gene identifier or by protein name or sequence to identify modified sites in a protein of interest. The record for each protein includes information about the types of domains present, phosphosites and acetylation sites identified by Mann's group, references supporting the existence of these modifications, and links to information about modification sites in other sources such as the Swiss-Prot and Phospho.ELM databases. For each modification site, there is information about predicted secondary structure, evolutionary conservation, dynamics of modification, and the biological context in which the modification was detected. The human dataset includes collections of mitochondrial phosphoproteins and proteins for which the phosphorylation state is regulated by epidermal growth factor (EGF) signaling; in addition, complete lists of all phosphoproteins are available for four bacterial species. Readers can use the phosphorylation site predictor to identify likely positions of phosphothreonine and phosphoserine residues or identify PHOSIDA motifs within a protein of interest. The "Background" section provides information on the methods used to predict phosphorylation sites, information on each of the organism-specific datasets, links to the published mass spectrometry analyses, instructions for downloading the datasets, and details about the sequence, structural, and evolutionary analyses of the phosphoproteins in the database.

(Free Site)

Phospho.ELM 

Phospho.ELM is a curated database of experimentally verified and manually annotated serine, threonine, and tyrosine phosphorylation sites in eukaryotic proteins. Search the database by protein or gene name or by Uniprot or Ensembl identifier to access information about phosphorylation sites in proteins of interest. Users may also select a kinase or a phosphopeptide binding domain from a drop-down menu to view proteins phosphorylated by a specific kinase such as MAPK1 or that contain phosphorylation sites recognized by a specific binding motif such as the Src SH2 domain, respectively. Users may submit a sequence query through the Phospho BLAST Search tool to identify portions of a particular protein that match phosphopeptides contained in the database. Each phosphoprotein's record includes its phosphorylation sites and their sequence contexts, links to PubMed references supporting the existence of each phosphorylation event, and the identity of the kinase(s) responsible for each modification. For most phosphoproteins, there are also links to interaction networks in NetworKIN, STRING, or PHOSIDA. Records also include information about each phosphoprotein's subcellular localization and the tissue(s) in which it is found, links to relevant BioCarta pathways, and information about binding partners in the MINT database. Version 8.2 (April 2009) contains 19,649 phosphorylation sites distributed amongst 4,687 proteins, and users can request access to a tab-delimited file containing all of these phosphorylation sites for academic or other non-commercial purposes.

(Free Site)

PhosphoPep 

PhosphoPep is a database of protein phosphorylation sites identified by mass spectrometry (MS) analysis; it includes data from human, fruit fly, nematode, and yeast. Each of the four organism-specific libraries may be searched for phosphopeptides that are present in proteins of interest or that match user-defined spectral data. Lists of proteins and pathways represented by phosphorylated peptides in each dataset are available for browsing. For each protein that contains one or more phosphorylated peptides, the sequence and position of each phosphorylation site within the protein, as well as the original MS data for each phosphopeptide, are provided. PhosphoPep enables users to access KEGG pathways, view STRING protein-protein interaction networks, identify predicted motifs with Scansite, or create a Cytoscape network for each phosphoprotein. The libraries of MS data are available for download, and the Usage Guide includes information about terms used in the database, including those used to describe the quality of the spectral data, and a downloadable tutorial.

(Free Site)

Phosphorylation Site Database 

The Phosphorylation Site Database, constructed and maintained by Peter J. Kennelly, Susannah Wurgler-Murphy, and Douglas M. King, provides information on prokaryotic proteins that undergo serine, threonine, or tyrosine phosphorylation. The database may be searched by the name of the protein or gene of interest, the gene or protein GenBank, SwissProt, or PIR accession number, the sequence of the phosphorylation site, the phosphorylated amino acid residue, or literature citation. All information in the database comes from the primary scientific literature.

(Free Site)

PhosphoSite 

This database of phosphorylated proteins is being curated by scientists at Cell Signaling Technologies (CST) and there are links to CST products related to the phosphorylated proteins on the pages. The information about the phosphorylated proteins is easy to access through the search interface. Information about the entire phosphoprotein, as well as additional details about specific phosphorylated residues are available. External links are also provided to selected online resources and tools. An online tutorial guides new users to the features of the site.

(Free Site)

Prosite 

Prosite, a searchable database of protein domains and functional sites, is part of the ExPASy group of proteomics databases and tools. Users may search by domain name to access functional, structural, and taxonomic information, as well as consensus sequences and alignments of individual sequences that represent a domain, such as SH2 or histidine kinase domains. Prosite will scan user-supplied protein sequence data to identify domains and motifs and determine to what family the protein belongs. Users may enter their protein sequences through the main page for a quick scan or through the advanced tool ScanProsite for more control over search parameters. Search results are returned as a list of conserved domains found in the input protein sequence and include both general information about each domain and information about specific proteins in which the molecular function or structure of a particular domain has been characterized. Prosite also provides information about the characteristics shared by proteins that contain a particular domain, so users can make predictions based on domain content and structure. Users can also access alignments that may contain hundreds of individual sequences to see the degree of sequence variability in homologous domains. The MyDomains Image Creator can be used to make customized domain cartoons for one's favorite real or hypothetical protein. The PRATT tool allows users to identify conserved domain patterns from groups of proteins that do not align by sequence.

(Free Site)

Protein Kinase Resource 

The Protein Kinase Resource has a new location. The new site has been updated and contains a useful collection of tools and data for aficionados of these central enzymes of signal transduction. An active and helpful "Protein Kinase Discussion Group" offers access to the know-how of other kinase researchers. The old PKR site will "expire" at the end of this year.

(Free Site)

Reactome 

The Reactome database, which provides a curated resource of core pathways and reactions in human biology, is being developed through a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium. Written by researchers and cross-referenced with with PubMed, GO, and the sequence databases at NCBI, Ensembl and UniProt, Reactome contains information on topics ranging from apoptosis to xenobiotic metabolism, including sections on cell cycle checkpoints, insulin receptor-mediated signaling, and the Notch signaling pathway.

(Free Site)

Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) 

"The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR." Over 10,000 searchable protein structures, interactively displayed in VRML, Java, Rasmol, Chime...even GIF! With its recent transfer from Brookhaven National Laboratory to The Research Collaboratory for Structural Bioinformatics, PDB promises to provide further innovations in macromolecular structure analysis.

(Free Site)

ROSPath 

ROSPath, a database being developed by researchers at the Center for Cell Signaling Research at Ewha Women's University, is intended to provide organized information pertaining to signaling mediated through reactive oxygen species.

(Free Site)

Scansite 

Scansite allows you to submit a protein sequence to search for binding motifs and phosphorylation sites. It is very easy to use and the output is clearly presented. Michael B. Yaffe and Lewis Cantley are the Project Directors.

(Free Site)

Stephen White Laboratory at UC Irvine 

The White laboratory, which conducts research concerning the folding and stability of membrane proteins, maintains various membrane and protein biophysics resources. The Membrane Protein Resources include a list of membrane proteins with known 3D structures, a searchable membrane protein topology database, and the Membrane Protein Explorer--a tool for examining the topology of membrane proteins. With beautiful images of protein structure, links to the Protein Data Bank, PubMed and numerous other useful sites, this site provides an invaluable resource for anyone interested in problems related to the structure of membrane proteins.

(Free Site)

The Human Protein Atlas 

The Human Protein Atlas is a database of human protein expression data from the Swedish Human Proteome Resource (HPR), a project that aims to produce monoclonal antibodies specific to every human protein and then use these antibodies to generate comprehensive expression data. The atlas includes histological data for about 5,000 proteins from 48 tissues, 20 cancer cell types, and 47 human cell lines. The database may be searched by protein name, or users can browse functional categories such as “kinases” or “G protein-coupled receptors.” Search results are returned as entries in a table, each of which includes links to external databases that contain information about the protein, the ID number of the antibody that recognizes the protein, and information about additional expression data that validate or contradict the histological data generated with the antibody. By navigating through the results, users can access the histological expression data obtained with each antibody in normal and cancer tissues and in cultured cells. Results from immunofluorescence, protein array, or Western blot assays used to verify the histological data can be accessed through color-coded links that indicate whether or not they support (green) or contradict (red) the histological data. In addition, users can also obtain detailed information for each protein, including ontology, cytological location, protein topology, transcript information, and links to Entrez Gene, EnsEMBL, and UniProt records. Information about how to purchase the antibodies is also available.

(Free Site)

The SH2 Domain 

A project of the lab of Piers Nash at the University of Chicago, this site offers a information about the human and mouse proteins with Src homology 2 (SH2) domains. There is information about the structures of many of these domains, the phenotypes of mouse knockouts, as well as information about the diseases with which proteins containing these domains have been implicated. The summary table provides information about the chromosomal locations of the human and mouse SH2-containing proteins, along with a handy list of synonyms for the proteins. Some links take the reader to the NCBI databases for additional information. A dendrogram of the human SH2 domains is organized into proteins with similar functions. The dendrogram and the sequence alignment are presented with an interface that relies on Flash and allows the reader to zoom in and out to explore the information more easily.

(Free Site)

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