ST NetWatch: Labs and People

Cellular Calcium Information Server
Mitsuhiko Ikura has created this website and database to organize and compare numerous sequence and structural information in the calcium research-related literature. The site includes databases for calmodulin target proteins, the cadherin superfamily, and the EF-hand protein superfamily.
Clapham lab
Members of the Clapham lab at Harvard University study cardiac signaling pathways, and they have made some resources concerning ion channels and calcium signaling available on the lab web site. These include comprehensive tables of information about transient receptor potential (TRP) channels,with separate tables for the TRPC, TRPM, and TRPV subfamilies, and a fourth table that combines information about the TRPA, TRPP, and TRPML classes of channels. These tables contain information about TRP family members, such as splice variants, disease models and mutations, agonists, inhibitors, interacting proteins, expression information, and a lot more. Videos posted on the site show confocal imaging of calcium waves in frog oocytes and an illustration of how to apply patch-clamping techniques to sperm. There is also an extensive review of calcium signaling.
Ehlers Lab
Mike Ehlers' lab at Duke University studies the role of protein trafficking in the formation and function of neuronal synapses. The "Research" section of the laboratory's Web site provides general resources about this topic, as well as results of the group's research. The "Presentations" section has collections of images and animations that illustrate the lab's research and includes topics such as endosomal trafficking, clathrin dynamics, and AMPA and NMDA receptor trafficking. The "Data and Images" section includes images, cartoons, and animations that illustrate the machinery of protein trafficking in neuronal dendrites and spines. Some of the slides are general enough to be appropriate as background material for those new to neuronal protein trafficking, but many provide experimental details that would also appeal to users familiar with the secretory pathway and endocytic recycling.
Eisen Lab
The Eisen lab uses DNA microarray technology to study gene expression and regulation. The site offers free to academic users the ability to download microarray analysis software and the ability to upload datasets to compare against other datasets using Clustermap. Access to other analysis tools are also provided. For those working with microarrays, this site may be quite useful.
Forsburg Lab
The Forsburg lab uses the fission yeast Schizosaccharomyces pombe to investigate the relationships between DNA replication, chromosome dynamics, and the cell cycle. In addition to providing a wealth of information on DNA replication and the fission yeast cell cycle, the site includes protocols and practical information for working with pombe as well as links to other web-based resources providing pertinent information.
Holmgren Lab
The Holmgren lab at Northwestern University studies the process of pattern formation during animal development. The lab focuses on the Hedgehog (Hh) signal transduction pathway and its role in the patterning of Drosophila. He shares short Protocols of frequently used laboratory methods. But, perhaps the best part of the site is the Glossary, which opens in a separate window. The Glossary includes not only definitions, but also signaling models of EGFR, Hedgehog, and Notch signaling, concepts in development, and developmenal models, a list of genes, and links to related sites.
Kuriyan Lab
Devoted to structural biology, the Kuriyan Lab web site provides structures for numerous molecules involved in cell signaling, including tyrosine kinases, serine/threonine kinases, and heme sensors, as well as structures of molecules involved in DNA replication. Associated information, links to publications, and movies are also available.
Neuronal Calcium Sensor Proteins
This is a site set up by the Bob Burgoyne lab at the University of Liverpoool to provide a resource of information on the Neuronal Calcium Sensor (NCS) family of calcium-binding proteins. The site includes all family members with up-to-date information on known structures and sequences. It has been set up with links to databases for each protein as well as links to searches for papers on interacting proteins and functions.
Shawn Thomas, a graduate student at the University of Illinois at Urbana-Champaign, has compiled and organized information pertaining to neuroscience, psychology, and pharmacology at Among other resources, the site includes charts of neuroactive substances, links and indexes of recent abstracts, and a metadatabase for the biological sciences.
Pawson Lab
Although Tony Pawson passed away in 2013 (see the Remembrance in Science Signaling), the information related to the projects that his lab studied continue to be available on his lab website. He focused on the modular domains that mediate signal transduction. There are pages on protein domains involved in protein-protein interactions and information about how specificity is achieved in signal transduction cascades. There are also links to information about mass spectrometry and links to the several research-related databases.
Rac Page
Information from the Lambeth lab regarding the structural analysis of the small GTPase Rac including a table summarizing the effects of point mutations on Rac interaction with NADPH oxidase.
Rel/NF-κB Transcription Factors
Thomas Gilmore, a professor of biology at Boston University, has created an online resource for the study of nuclear factor-κB (NF-κB) transcription factors. The site includes an introduction to this family of transcription factors and an overview of their regulation. Links to GenBank sequences and Protein Data Bank (PDB) structures for NF-κB transcription factor subunits and the proteins that directly regulate their activity (IKK, IκB) in response to upstream signaling events are available. A large number of compounds, biomolecules, and biological agents or processes, such as infections and stresses, reported to inhibit or promote NF-κB activity are listed here along with references supporting their effect on NF-κB. Users can also access lists of genes that are transcriptionally regulated by NF-κB transcription factors, a list of mouse knockout lines in which NF-κB transcription factors or their regulators have been disrupted, a list of diseases with which aberrant NF-κB activity has been associated, and a list of proteins that interact with NF-κB proteins or their regulators. PubMed links to citations that support the inclusion of each entry in these sections are provided, and the site has an extensive list of publications on NF-κB transcription factors.
Rune Linding: Research Group
The laboratory of Rune Linding is a computational biology research group at the Technical University of Denmark. The laboratory focuses on signal transduction networks in disease and is part of the Integrative Network Biology Initiative (INBI), a consortium of systems and network biologists studying cancer metastasis. The site includes an overview of the laboratory’s ongoing research in integrative network biology, network evolution, signaling dynamics, and pharmacological targeting of networks. The site also provides access to computational tools developed by the Linding lab: NetworKIN, an algorithm that predicts kinase-substrate relationships, and NetPhorest, an online tool for matching phosphorylated sequences with kinases and predicting phosphorylation-dependent protein-protein interactions.
Sheen Lab
Jen Sheen's group is part of the NSF 2010 Arabidopsis Project and has created teaching materials and protocols, as well as made data available regarding the signaling pathways that control plant responses to growth and stress hormones, nutrients, environmental stresses, and pathogens. The site is rich in images, Power Point slides, and explanatory information. There is a section highlighting calcium-dependent protein kinase (CDPK) signaling, plus sections highlighting the lab's research on cytokinin, auxin, immunity, and abscisic acid and stress signaling.
Synapse Web
Synapse Web, created by the laboratory of Kristen M. Harris from the Program in Synapses & Cell Signaling at the Medical College of Georgia, provides an abundance of information concerning the structural basis of synaptic function. The site includes an atlas of ultrastructual neurocytology (created by Dr. Josef Spacek), beautiful images of brain structures and cells (from Nissl-stained sections of hippocampus to Golgi-stained pyrmaidal cells to 3D reconstructions of dendritic spines), tutorials, and a suite of tools for the analysis and 3D reconstruction of structures from serial sections.
The Clickable Guard Cell
Guard cells are parenchymal cells that form stomata, the pores that mediate gas exchange in plants. A pair of guard cells regulates the aperture of each stoma by responding to environmental and hormonal cues, a system that is a popular model for studying plant signal transduction. The Clickable Guard Cell is an interactive review of guard cell biology from the laboratory of Julian Schroeder at the University of California, San Diego. This extensive review features two interactive figures that illustrate the signaling pathways activated by abscisic acid (ABA) and blue light. Clicking on a component in either pathway reveals information about the component, including a link to the entry for the gene encoding the component in The Arabidopsis Information Resource and links to key publications characterizing the function of the component. Users may also jump to the place in the review where that component is discussed. A third, noninteractive figure illustrates the roles of ion channels in ABA signaling.
The 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.
The Wnt Homepage
An extensive collection of information about Wnt proteins in many organisms, Wnt signaling components, Wnt literature, and assays and tools for studying Wnt signaling. The site is maintained by Roel Nusse and the updates are clearly indicated.
Woodgett Lab
The Woodgett lab provides an information resource on protein kinases and various signal transduction pathways. An extremely user-friendly site, with signaling maps, Wnt pathway Flash movies, a kinase quiz, laboratory protocols and many useful links. The signaling maps include stress activated protein kinase pathways, the protein kinase B (also called Akt) in phosphatidylinositol 3-kinase cell survival pathway, and Wnt signaling pathways.