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 Encyclopedia (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)

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)

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)

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)

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)

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)

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)

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)

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)

Phospho.ELM 

The Phospho.ELM provides a search interface into a database of manually curated information about protein phosphorylation. The exact residues, the sequence context of the phosphorylated residue, and the kinases responsible are all supplied, along with links to selected external reference information (PubMed, ExPasy). With searches for phosphorylated protein, kinase, or binding motif, Phospho.ELM allows the user to easily retrieve information. Phospho.ELM version 3.0 contains information about 1552 substrate entries from multiple species.

(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)

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)

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)

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)

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)

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 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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