Useful Web Resources
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.
