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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 stke.sciencemag.org
Signal transduction knowledge environment: resources and information on signal transduction, Science Magazine and Stanford University. Requires Subscription.
BIND - The Biomolecular Interaction Network bond.unleashedinformatics.com
Biomolecular Interaction Network Database serves full descriptions of interactions of proteins, nucleic acids and small molecules.
BioCarta - Charting Pathways of Life www.biocarta.com/search/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 & Cells Online Pathfinder Encyclopedia www.copewithcytokines.org
Cytokines & Cells Encyclopedia, University of Munich.
GPCRDB: Information system for G protein-coupled receptors (GPCRs) www.gpcr.org/7tm
Information system for G protein-coupled receptors.
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
Collaborative effort to build integrated, multidisciplinary models of neurons and neural systems, Yale University.
Bioinformatics & Biological Computing bip.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/home/home.do
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.shtml
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.predictprotein.org
PredictProtein is a service for sequence analysis and structure prediction, Heidelberg.
Genome Sequencing Center genome.wustl.edu
Genome Sequencing Center, Washington University
GeneCards Homepage www.genecards.org
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.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.
TIGEM Telethon Institute of Genetics and Medicine www.tigem.it
Links to resources for expressed sequence tags analysis, University of Brescia.

Online Publications And Literature Search Engines

Entrez PubMed www.ncbi.nlm.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.plos.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 atlasgeneticsoncology.org
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 www.ncbi.nlm.nih.gov/sites/entrez?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/ac/index.php
Human Gene Mutation Database, Institute of Medical Genetics, Cardiff.
OMIM Locus-specific mutation database links www.ncbi.nlm.nih.gov/Omim/allresources.html#LocusSpecific
Links to a number of locus specific mutation databases, N.I.H.
Disease Genes www.ncbi.nlm.nih.gov/disease/
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

JAX Mice Database jaxmice.jax.org/query/
Source of mouse strains with transgenes, or with targeted or chemically-induced mutations, The Jackson Laboratory.

Genome Databases

The Sanger Institute: Human Genome Project www.sanger.ac.uk/about/history/hgp/
The human genomic research program, Sanger Center.
TIGR Human Gene Index compbio.dfci.harvard.edu/tgi/
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 www.yeastgenome.org
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.
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