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Amos' WWW links page

Release 5.51 / March 25, 2003 (>1000 links!!)

This list contains almost exclusively pointers to information sources for life scientists with an interest in biological macromolecules. Links to protein sequence, 3D structure and 2D-gel analytical tools are provided on the ExPASy server, and more specifically from its Proteomics tools page. Links to Geneva and Swiss biological servers, institutes, etc. are on the Local page of ExPASy. Finally, if you don't find what you want here, do not forget to use our BioHunt molecular biology information search engine.

If you think that I should add a specific link, then send me the relevant details, but I reserve the right to choose what I want to include in this page!

Notes:


Quick jump to the following topics:
Proteins db | 3D structure db | 2D-PAGE & MS db | DNA/RNA db | Carbohydrates db | Organisms specific db | Human mutation db | Genes/proteins specific db | PTM db | Phylogenetics db | Microarrays db | Patents | References | Dict., primers & nomenclat. | Biol. soft. & db catalogs | Gateways | Biol. journals & publishers | Biol. societies | Biocomputing servers | Biotech. companies | Bioinformatics companies | Java in BioMol | Misc. medical ref. sites | Misc. scientific ref. sites | Misc. general ref. sites | News | Computing | Recreational | Miscellaneous

Biolinks

Protein and associated topics databases
  • Swiss-Prot - Swiss-Prot annotated protein sequence db
  • Kabat - Kabat db of sequences of proteins of immunological interest
  • PMD - Protein Mutant db

  • InterPro - Integrated Resources of Proteins Domains and Functional Sites
  • PROSITE - PROSITE dictionary of protein sites and patterns
  • BLOCKS - BLOCKS db
  • Pfam - Protein families db (HMM derived) [Mirror at St. Louis (USA)]
  • PRINTS - Protein Motif fingerprint db
  • ProDom - Protein domain db (Automatically generated)
  • PROTOMAP - An automatic hierarchical classification of Swiss-Prot proteins
  • SBASE - SBASE domain db
  • SMART - Simple Modular Architecture Research Tool
  • TIGRFAMs - TIGR protein families db

  • BIND - Biomolecular Interaction Network db
  • DIP - Db of Interacting Proteins
  • MINT - Molecular INTeractions
  • ProNet - Protein-Protein interaction db
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Protein 3D structure and associated topics databases
  • PDB - Protein Data Bank
  • BioMagResBank - Repository for data on proteins, peptides, and nucleic acids from NMR spectroscopy
  • SWISS-MODEL Repository - Automatically generated protein models db
  • ModBase - Db of comparative protein structure models
  • CATH - UCL BSM structural classification of proteins
  • SCOP - Structural classification of proteins [Mirror at USA | Israel | Singapore | Australia]
  • Mol_R_Us - Molecules R Us, browser for PDB
  • BMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server
  • PRESAGE - Collaborative resource for structural genomics
  • ReLiBase - Receptor/ligand complexes db [Mirror in USA]
  • TOPS - Protein topology atlas
  • CCDC - Cambridge Crystallographic Data Center (Cambridge Stuctural Db (CSD))
  • HSSP - Homology-derived secondary structure of proteins db
  • MutaProt - Comparison of PDB files which differ by point mutations

  • SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
  • BioImage - Biological image db (contains imaging data on macromolecules)
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Protein 2D-PAGE and MS databases
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Nucleotide and associated topics databases
  • EMBL - EMBL Nucleotide sequence db (EBI)
  • Genbank - GenBank Nucleotide Sequence db (NCBI)
  • DDBJ - DNA Data Bank of Japan
  • dbEST - dbEST (Expressed Sequence Tags) db (NCBI)
  • dbSTS - dbSTS (Sequence Tagged Sites) db (NCBI)

  • NDB - Nucleic Acid Databank (3D structures)
  • BNASDB - Nucleic acid structure db from University of Pune

  • AsDb - Aberrant Splicing db
  • ACUTS - Ancient conserved untranslated DNA sequences db
  • Codon Usage Db
  • EPD - Eukaryotic Promoter db
  • HOVERGEN - Homologous Vertebrate Genes db
  • IMGT - ImMunoGeneTics db [Mirror at EBI]
  • ISIS - Intron Sequence and Information System
  • RDP - Ribosomal db Project
  • gRNAs db - Guide RNA db
  • PLACE - Plant cis-acting regulatory DNA elements db
  • PlantCARE - Plant cis-acting regulatory DNA elements db
  • sRNA db - Small RNA db
  • ssu rRNA - Small ribosomal subunit db
  • lsu rRNA - Large ribosomal subunit db
  • 5S rRNA - 5S ribosomal RNA db
  • tmRNA Website
  • tmRDB - tmRNA dB
  • tRNA - tRNA compilation from the University of Bayreuth
  • uRNADB - uRNA db
  • RNA editing - RNA editing site
  • RNAmod db - RNA modification db
  • SOS-DGBD - Db of Drosophila DNA sequences annotated with regulatory binding sites
  • TelDB - Multimedia Telomere Resource
  • TRADAT - TRAnscription Databases and Analysis Tools
  • Subviral RNA db - Small circular RNAs db (viroid and viroid-like)

  • MPDB - Molecular probe db
  • OPD - Oligonucleotide probe db
  • VectorDB - Vector sequence db (seems dead!)
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Carbohydrates resources
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Species specific databases
Human
Vertebrates
Mitochondrion and chloroplast
  • GOBASE - Organelle Genome Database
  • MitoDat - Mendelian Inheritance and the Mitochondrion db (mitochondrial nuclear genes)
  • MITOMAP - Human mitochondrial genome db
  • MmtDB - Metazoa mitochondrial DNA variants db
  • MitBASE - Integrated mitochondrial DNA db
  • MitBASE-Pilot - Db of S.cerevisiae nuclear genes involved in mitochondrial biogenesis
  • HvrBase - Primates mtDNA control region sequences compilation
  • MOUSE - Mitochondrial and Other Useful SEquences (human and apes mit. DNA db)

  • C.caldarium - Cyanidium caldarium strain RK1 chloroplast genome
Insects
Invertebrates
Plants
Fungi
Bacteria
Archaea
Viruses and phages
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Human mutation databases/resources
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Gene(s)/protein(s) specific databases/resources
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Post-translational modifications databases and resources
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Phylogenetics databases and resources
  • TreeBASE - Relational db of phylogenetic information
  • The Tree of life - Collection of WWW pages on phylogeny and biodiversity of organisms
  • RDP - Ribosomal db Project
  • ICB - Identification and Classification of Bacteria
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Microarray databases and resources
  • ArrayExpress - MicroArray informatics at the EBI
  • ChipDB - Gene expression db
  • ExpressDB - Yeast and E.coli RNA expression db
  • GeneX - Gene Expression project
  • GEO - Gene Expression Omnibus
  • RAD - RNA abundance db
  • SMD - Stanford microarray db
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Patents databases
  • DPD - DNA Patent db
  • Ag Patents - Agricultural Biotechnology patents from the USDA

  • USPTO patent db - USA Patent and Trademark Office patent db
  • Esp@cenet - Patent information database from the European Patent Office (worldwide coverage)
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References (bibliographic databases)
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Dictionaries, primers, courses, nomenclature, etc.
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Biological software and databases catalog servers
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Gateways (portals) to Life Sciences resources
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Biological journals and publishers
Resources that links to journals home pages
Publishers
Bioinformatics journals and newsletters
Genomic newsletters
Miscellaneous
Biotechnology trade journals
General science journals
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Some biological societies and organizations
  • APS - American Peptide Society
  • ASCB - The American Society for Cell Biology
  • ASHG - American Society of Human Genetics
  • ATCC - American Type Culture Collection
  • Biochemical Society
  • BSA - Botanical Society of America
  • CSBMCB - Canadian Society of Biochemistry and Molecular and Cell Biology
  • DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
  • EGF - European Genetics Foundation
  • EMBO - European Molecular Biology Organization
  • ESEB - European Society for Evolutionary Biology
  • ESHG - European Society of Human Genetics
  • FAOBMB - Federation of Asian and Oceanian Biochemists and Molecular Biologists
  • FASEB - Federation of American Societies for Experimental Biology
  • FEBS - Federation of European Biochemistry Societies
  • FGM - Foundation for Genetics Medicine
  • HUGO - HUman Genome Organization
  • HUPO - HUman Proteome Organization
  • IUBMB - International Union of Biochemistry and Molecular Biology
  • IUPAC - International Union of Pure and Applied Chemistry
  • JBS - Japanese Biochemical Society
  • MSA - Mycological Society of America
  • PPI - Plasma Proteome Institute
  • PRF - Protein Research Foundation
  • SDB - Society for Developmental Biology
  • SGM - Society for General Microbiology
  • SICB - Society for Integrative and Comparative Biology

  • DOI - Digital Object Identifier foundation

  • BioJava Project - International association of developers of Java tools for bioinformatics
  • Bioperl Project - International association of developers of Perl tools for bioinformatics
  • Biopython Project - International association of developers of Python tools for bioinformatics
  • Bioxml Project - International association of developers of XML tools for bioinformatics
  • The Open lab - International collaboratory for open-sources bioinformatics R&D
  • ISCB - International Society for Computational Biology
  • OMG LSR - Object Management Group Life Science Research task force
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Biocomputing servers homepages
Europe
  • EBI - European Bioinformatics Institute
  • EMBnet - European Molecular Biology Network
  • EMBL - EMBL Biocomputing unit

  • SIB - Swiss Institute of Bioinformatics
  • EMBnet CH - Switzerland EMBnet node
  • ISREC - ISREC bioinformatics group (Lausanne / Swizerland)
  • CBRG - Computational Biochemistry Research Group (Zurich / Switzerland)

  • INFOBIOGEN - GIS INFOBIOGEN; France EMBnet node
  • ABIM - Atelier BioInformatique (Marseille / FR)
  • B3E - Bioinformatique/Biostatistique/Biomathematique/Epidemiologie (Paris / FR)
  • CNRS GDR 1029 - Informatique et génomes
  • Genethon - Genethon (Evry / FR)
  • GeneStream - Institut de Génétique Humaine (Montpellier / FR)
  • GENOSCOPE - Centre National de Séquencage (Evry / FR)
  • GenoStar - Consortium for the development of a bioinformatic platform
  • IGS - Information Génétique et Structurale (Structural and Genetic Information Laboratory) (Marseille / FR)
  • IMPG - Action Informatique Mathématique Physique pour la Génomique
  • Pasteur - Institut Pasteur (Paris / FR)
  • PBIL - Pole Bio-informatique Lyonnais (Lyon / FR)
  • DESS EGOISt - DESS Etude des Génomes: outils informatiques et statistiques
  • DESS IAB - DESS Informatique Appliquée a la Biologie

  • SEQNET - SEQNET; U.K. EMBnet node
  • Sanger - Sanger Centre (Hinxton / U.K.)
  • HGMP-RC - MRC HGMP Resource Centre (Hinxton / U.K.)
  • Beowulf Genomics - Wellcome Trust genome sequencing initiative WWW site
  • BMM - Biomolecular Modelling laboratory at ICRF (London / U.K.)
  • Brunel Bioinformatics Group - Bioinformatics Group in the Department of Biological Sciences at Brunel University (U.K.)
  • BSM - Biomolecular Structure and Modelling group at UCL (London / U.K.)
  • Manchester - Manchester University Bioinformatics unit (U.K.)
  • RIO - Roslin Institute Online (U.K.)

  • GeniusNet - DKFZ Biocomputing Service Group; Germany EMBnet node
  • GSF AG BIODV - Software Development for Molecular Biology at the GSF Institut fuer Sauegetiergenetik
  • GSC - Genome Sequencing Center (Iena / Germany)
  • MDC:Bioinf - Department of Bionformatic of the Max Delbruck Center for Molecular Medicine (Germany)
  • MIPS - Munich Information Centre for Protein Sequences (Germany)
  • VSNS BCD - Virtual School of Natural Sciences Biocomputing Division from the University of Bielefeld (Germany)

  • BCC - Vienna University Department for Biocomputing; Austria EMBnet node
  • BEN - Belgium EMBnet node
  • BIOBASE - Denmark EMBnet mode
  • CBS - Center for Biological Sequence Analysis (Technical University of Denmark)
  • CSC BioBox - CSC; Finland EMBnet node
  • IMBB - Greece EMBnet node
  • ABC - Agricultural Biotechnology Center (Budapest / Hungary)
  • INCBI - Irish National Center for Bioinformatics; Ireland EMBnet node
  • TigemNet - Telethon Institute of Genetics and Medicine Bioinformatics resources (Italy)
  • CMBI - Center for Molecular and Biomolecular Bioinformatics; Netherland EMBnet node
  • BIO - Norway EMBnet node
  • IBB - Institute of Biochemistry and Biophysics (Warsaw); Poland EMBnet node
  • Pen - Portugal EMBnet Node
  • Belozersky Institute - Belozersky Institute (Moscow); Russia EMBnet node
  • MGS - Molecular Biological Server (Novosibirsk / Russia)
  • CNB - Centro Nacional de Biotecnologia; Spain EMBnet node
  • BMC - BioMedical Centre at Uppsala; Sweden EMBnet node
  • KISAC - Karolinska Institute (KI) Sequence analysis facility
  • LCB - Linnaeus Centre for Bioinformatics
  • SBC - Stockholm Bioinformatics Center
  • NBN - National Bioinformatics Node; Turkey EMBnet node
  • Bioserver - Biocomputing server at Bogacizi University (Turkey)
USA and Canada
  • NCBI - National Center for Biotechnology Information

  • ABCC - Advanced Biomedical Computing Center at the NCI
  • ACGT - Advanced Center for Genome Technology at the University of Oklahoma
  • BCM HGC - Baylor College of Medicine Human Genome Center
  • BDGP - Berkeley Drosophila Genome Project
  • BioTech - BioTech biology/chemistry educational resource and research tool
  • BIC - The Biotechnology Information Center
  • BMERC - Biomolecular Engineering Research Center
  • CBIL - Computational Biology and Informatics Laboratory at the University of Pennsylvania
  • CUBIC - Columbia University Bioinformatics Center
  • GSC - Genome Sequencing Center at Washington University
  • HGP Columbia - Human Genome Project at Columbia University
  • IBC - Washington University Institute for Biomedical Computing
  • LANL - Los Alamos National Laboratory (LANL) center for human genome studies
  • LBNL - Lawrence-Berkeley National Laboratory (LBNL) Human Genome informatics group
  • MBCR - Molecular Biology Computational Resource at Baylor College of Medicine
  • NCGR - National Center for Genome Resources
  • NIH - NIH molecular biology
  • SAGC - The San Antonio Genome Center
  • TIGR - The Institute for Genome Research
  • UCLA - UCLA Bioinformatics Institute
  • Biocomputing at Whitehead Institute for Biomedical Research
  • WICGR - Whitehead Institute Center for Genome Research

  • CBR - Canadian Bioinformatics Resource
  • BiSC - Bioinformatics Supercomputing Centre
Asia
  • APBioNet - Asia-Pacific Bioinformatics network

  • BIC-JNU - Bioinformatics Center of Jawaharlal Nehru University
  • DIC - University of Pune (India) Bioinformatics Centre

  • Japanese GenomeNet
  • NIG - National Institute of Genetics of Japan
  • KDRI - Kazusa DNA Research Institute

  • CBI - Peking Center of Bioinformatics; Chinese EMBnet node
  • MICRO-NET - Microbial Information Network of China
  • HKBIC - Hong Kong Bioinformatics Center

  • BRIC - Biological Research Information Center (Korea)
  • BIC - BioInformatics center of the National University of Singapore
Australia
  • APBioNet - Asia-Pacific Bioinformatics network

  • ANGIS - Australian National Genomic Information Service
  • ANU - Australian National University Bioinformatics group
  • APAF - Australian Proteome Analysis Facility
Others
  • HUJI - Hebrew University of Jerusalem genomic and bioinformatics server
  • Weizmann Bioinfo/BCU - Weizmann Institute of Science Bioinformatics and Biological Computing

  • SANBI - South African BioInformatics Institute

  • BDT - Base de Datos Tropical (Sao Paulo / Brazil)
  • LBI - Bioinformatics Laboratory at the Institute of Computing of the University of Campinas (Brazil)

  • ICCBnet - International Center for Cooperation in Bioinformatics Network
  • ICGEB - International Center for Genetic Engineering and Biotechnology (Trieste / Italy)
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Biotechnology and pharmaceutical companies
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Bioinformatics companies
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BioMolecular Java applications and demos
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Other links

Miscellaneous medical references sites
  • HON - The Health On the Net foundation server
  • Hardin MD - Hardin meta directory of Internet health sources
  • Mednav.com - Guide to the Internet medicine
  • MedWeb - Medical links site

  • FDA CDER - FDA Center for Drugs Evaluation and Research
  • NLM - National Library of Medicine

  • MedicineNet - Medical Reference Site
  • MMRL - Multimedia Medical Reference Library
  • OMD - On-line medical dictionary (on CancerWEB)
  • OMNI - Organising Medical Networked Information
  • Medline Plus - NLM list of resources for health questions
  • ORPHANET - Resource dealing with rare diseases and orphan drugs
  • ORD - Office of Rare Diseases
  • ReutersHealth - Reuters Medical News
  • PharmInfoNet - Pharmaceutical Information Network
  • NMDWD - New Medicines in Development WebDatabase
  • Prous Science - Medical and drug information provider
  • TOXNET - Toxicology, hazardous chemicals and related areas db
  • Visible Human at EPFL - EPFL server for the images of the "Visible Human" NLM project

  • DrugDB - Db of information about drugs
  • Electronic Orange Book - FDA list of approved drug products
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Miscellaneous scientific references sites
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Miscellaneous general references sites
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News
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Computing-related links
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Recreational links
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Miscellaneous
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Disclaimer

This list is not supposed to be complete, it reflects my (Amos Bairoch) interests and will list servers that I find useful and up to date.

This page has received an award from SciCentral


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