Signal Transduction Research

AfCS-Nature Signaling Gateway www.signaling-gateway.org

The AfCS-Nature Signaling Gateway is a comprehensive resource for information about cell signaling, Alliance for Cell Signaling and the Nature Publishing Group.

Scansite scansite.mit.edu

Scansite predicts phosphorylation sites and specific domain-binding regions within proteins, MIT.

NetPhos 2.0 Server www.cbs.dtu.dk/services/NetPhos

Neural network predictions of phosphorylation sites in eukaryotic proteins, Technical University of Denmark.

Kinase.com www.kinase.com

Analyses of protein kinases from human, yeast, worm and fly.

AAAS | Science's STKE www.stke.org

Signal transduction knowledge environment: resources and information on signal transduction, Science Magazine and Stanford University. Requires Subscription.

Protein Kinase pkr.sdsc.edu/html/index.shtml

Protein Kinase Resource: the genetics, enzymology, and molecular properties of protein kinases, University of California San Diego.

BIND - The Biomolecular Interaction Network www.bind.ca

Biomolecular Interaction Network Database serves full descriptions of interactions of proteins, nucleic acids and small molecules.

BioCarta - Charting Pathways of Life www.biocarta.com/genes/index.asp

"Open source" resource providing online maps depicting selected signaling pathways.

Cell Cycle Regulated Yeast Genes genome-www.stanford.edu/cellcycle

Identification of yeast genes whose mRNA levels are regulated by the cell cycle, Stanford.

Horst Ibelgaufts'COPE: Cytokines Online Pathfinder Encyclopaedia www.copewithcytokines.de/cope.cgi?001441

Cytokines online encyclopedia, University of Munich.

The Nuclear Receptor Resource nrr.georgetown.edu/nrr/NRR1.html

Nuclear Receptor Resource: a collection of databases on the nuclear receptor superfamily, Georgetown University.

GPCRDB: Information system for G protein-coupled receptors (GPCRs) www.gpcr.org/7tm

Information system for G protein-coupled receptors.

Wnt Homepage www2.stanford.edu/~rnusse/wntwindow.html

Wnt gene homepage, Stanford.

NetOGlyc 3.1 Server www.cbs.dtu.dk/services/NetOGlyc

Predictions of GalNAc O-glycosylation sites in mammalian proteins, Technical University of Denmark.

SenseLab senselab.med.yale.edu/senselab

Collaborative effort to build integrated, multidisciplinary models of neurons and neural systems, Yale University.

Bioinformatics & Biological Computing bioinformatics.weizmann.ac.il

Extensive annotations of ‘hot molecules’ that may play crucial roles in common diseases, Weizmann Institute.

Antibody Resources

Antibody Resource Page: Find Monoclonal and Polyclonal Antibodies www.antibodyresource.com

Clearinghouse for locating specific antibodies and immunology resources.

ATCC: The Global Bioresource Center www.atcc.org

ATCC catalog of cell lines including hybridomas that produce a broad spectrum of antibodies

Proteomic/Genomic Tools

ExPASy Proteomics Server www.expasy.ch

Proteomic and genomic databases and tools from the Swiss Bioinformatics Institute, home of Swiss Prot.

The RCSB Protein Data Bank www.rcsb.org/pdb

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

SDSC Biology Workbench workbench.sdsc.edu

Biology Workbench, an integrated search, modeling and analysis platform that accesses all major protein and nucleic acid databases, University of Illinois

NCBI GenBank Overview www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html

GenBank, an annotated database of all publicly available DNA sequences, N.I.H.N.L.M.

NCBI BLAST Overview www.ncbi.nlm.nih.gov/BLAST/blast_overview.html

BLAST (Basic Local Alignment Search Tool), a set of search programs for identifying sequence similarities between protein and nucleotide sequences, N.I.H.N.L.M.

PredictProtein: structure prediction and sequence analysis www.embl-heidelberg.de/predictprotein/predictprotein.html

PredictProtein is a service for sequence analysis and structure prediction, Heidelberg.

Pfam: Protein Search (Saint Louis) pfam.wustl.edu/hmmsearch.shtml

Tool for analyzing the domain structure of protein sequences, PFAM consortium: Sanger Centre, Washington University, Karolinska Institute.

Genome Sequencing Center genome.wustl.edu

Genome Sequencing Center, Washington University

GeneCards Homepage bioinfo.weizmann.ac.il/cards

GeneCards: a database of human genes, their products and their involvement in disease, Weizmann Institute

Whitehead Institute for Biomedical Research www.wi.mit.edu

Online links to molecular sequence analysis tools for nucleotides and proteins, Whitehead Institute.

KEGG: Kyoto Encyclopedia of Genes and Genomes www.genome.ad.jp/kegg

Computerized effort to model molecular interactions, Kyoto University.

Human Unidentified Gene-Encoded Large Proteins www.kazusa.or.jp/huge/index.html

Sequence database of long (>4 kb) human cDNAs, Kazusa DNA Research Institute.

Gateways To Online Links

San Diego Supercomputer Center: Delivering Cyberinfrastructure www.sdsc.edu

Excellent compendium of tools and resources for molecular biology and proteomics, University of California San Diego.

Cell and Molecular Biology Online www.cellbio.com

Informational resources for cellular and molecular biology.

JustBio www.mbshortcuts.com/index.shtml

Molecular Biology Shortcuts, links to molecular and cellular biology methods and databases.

TIGEM Telethon Institute of Genetics and Medicine www.tigem.it

Links to resources for expressed sequence tags analysis, University of Brescia.

Cytokine Family Database cytokine.medic.kumamoto-u.ac.jp/CFC/CFC-links.html

Links to cytokine, chemokine and related resources, Kumamoto University.

Online Publications And Literature Search Engines

Entrez PubMed www.ncbi.nih.gov/entrez/query.fcgi?db=PubMed

NLM’s search service to citations in MEDLINE, with links to online journals and other related databases, N.I.H.

PubCrawler Web Service pubcrawler.gen.tcd.ie/

Free “alerting” service that scans daily updates to the NCBI, Medline and GenBank databases.

Public Library of Science www.publiclibraryofscience.org

Effort to make the world's scientific and medical literature freely accessible to scientists and to the public around the world.

Disease And Mutation Databases

KinMutBase bioinf.uta.fi/KinMutBase

Database of disease-causing mutations in tyrosine kinase domains, links to other mutation databases, University of Tampere.

Atlas Chromosomes in Cancer www.infobiogen.fr/services/chromcancer/index.html

Atlas of Genetics and Cytogenetics in Oncology and Haematology, dedicated to biological and molecular aspects of cancer and cancer-prone diseases.

OMIM - Online Mendelian Inheritance in Man www4.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

Online Mendelian Inheritance in Man: catalog of human genes and genetic disorders, N.I.H.

The Human Gene Mutation Database (HGMD) www.hgmd.cf.ac.uk/hgmd0.html

Human Gene Mutation Database, Institute of Medical Genetics, Cardiff.

OMIM Locus-specific mutation database links www4.ncbi.nlm.nih.gov/Omim/Index/mutation.html

Links to a number of locus specific mutation databases, N.I.H.

Disease Genes www.ncbi.nlm.nih.gov/Disease_Genes/m97hdt0.html

Positionally cloned human disease genes, N.I.H.

CGAP Collaboration www.ncbi.nlm.nih.gov/ncicgap

Cancer Genome Anatomy Project: database of the genes responsible for cancer, N.I.H.

Knockout And Transgenic Mice

Database Of Gene Knockouts www.bioscience.org/knockout/knochome.htm

List of those genes which have been ablated in mice and the phenotypic effects of these knockouts.

Transgenic Home Page www.ornl.gov/TechResources/Trans/hmepg.html

Transgenic and targeted mutant animal database, Oak Ridge National Laboratory.

JAX Mice Database jaxmice.jax.org/jaxmice-cgi/jaxmicedb.cgi

Source of mouse strains with transgenes, or with targeted or chemically-induced mutations, The Jackson Laboratory.

Genome Databases

The GDB Human Genome Database www.gdb.org/gdb/

Human Genome Project database, Toronto.

The Sanger Institute: Human Genome Project www.sanger.ac.uk/HGP

The human genomic research program, Sanger Center.

TIGR Human Gene Index www.tigr.org/tdb/tgi/hgi

TIGR human gene index.

Mitomap www.mitomap.org

Human mitochondrial genome, Emory University.

MGI 3.3 - Mouse Genome Informatics www.informatics.jax.org

The mouse genome, Jackson Laboratory.

Berkeley Drosophila Genome Project www.fruitfly.org

Drosophila genome project, Berkeley.

The Sanger Institute: C. elegans Project www.sanger.ac.uk/Projects/C_elegans

C. elegans genome, Sanger Center.

Saccharomyces Genome Database genome-www.stanford.edu/Saccharomyces

S. cerevisiae genome, Stanford.

The Enhanced Microbial Genomes Library pbil.univ-lyon1.fr/emglib/emglib.html

Completely sequenced bacterial genomes and the yeast genome, Universite Claude Bernard, Lyon.

Miscellaneous

Prolysis delphi.phys.univ-tours.fr/Prolysis

Proteases and protease inhibitors, University of Tours, France.