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Life Science Directory

(formerly known as Amos' WWW links page)
Quick jump to the following topics:
Protein db | 3D structure db | 2D-PAGE & MS db | DNA/RNA db | Carbohydrates db | Species specific db | Human mutation db | Genes/proteins specific db | PTM db | Phylogenetics db | Gene expression db | Patents | References | Dict., protocols & nomenclat. | Biol. soft. & db catalogs | Gateways | Biol. journals & publishers | Biol. societies | Biocomputing servers | Biotech. companies | Bioinformatics companies | Misc. medical ref. sites | Misc. scientific ref. sites

Protein related databases
  • UniProt - the universal protein resource (including UniProtKB -Swiss-Prot and TrEMBL-, UniRef, UniParc)
  • Around UniProtKB - links to related databases and portals
    • HAMAP SIB logo - Portal to microbial UniProtKB/Swiss-Prot entries
    • SwissVar SIB logo - Portal to human diseases and variant information in UniProtKB/Swiss-Prot
    • UniPathway - Metabolic pathways database
    • ViralZone SIB logo - Portal to viral UniProtKB/Swiss-Prot entries
    • HPI - Human Proteomics Initiative SIB logo
    • PPAP - Plant Proteome Annotation Project SIB logo
    • Tox-Prot - Toxin Annotation Project SIB logo
  • Swiss Human Plasma protein dataset SIB logo - Novartis/Geneprot MicroProt2 dataset from Human Plasma samples
  • NCBI protein resources

  • InterPro - Integrated Resources of Proteins Domains and Functional Sites
  • PROSITE SIB logo - Database of protein families and domains
  • BLOCKS - BLOCKS db
  • Gene3D - Structural and Functional Annotation of Protein Families
  • Panther - Functional classification system
  • Pfam - Protein families db (HMM derived) [Mirrors at JFRC (USA), CCBB (South Korea) Institute, UK, Karolinska Institutet (Sweden)]
  • PIRSF - Protein classification system
  • PRINTS - Protein Motif fingerprint db
  • ProDom - Protein domain db (Automatically generated)
  • SBASE - SBASE domain db
  • SMART - Simple Modular Architecture Research Tool
  • SUPERFAMILY - Library of profile HMMs representing all proteins of known structure
  • STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
  • TIGRFAMs - TIGR protein families db
  • BIND - Biomolecular Interaction Network Database
  • DIP - Database of Interacting Proteins
  • MINT - Molecular INTeraction database
  • HPRD - Human Protein Reference Database
  • IntAct
  • BioGRID - General Repository for Interaction Dataset
  • PPI - JCB Protein-Protein Interaction Website
  • PMD - Protein Mutant db
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Protein 3D structure related databases
  • PDB - Protein Data Bank
  • PDBTM - Protein Data Bank of Transmembrane Proteins
  • BioMagResBank - Repository for data on proteins, peptides, and nucleic acids from NMR spectroscopy
  • SWISS-MODEL Repository SIB logo - Automatically generated protein models db
  • ModBase - Db of comparative protein structure models
  • CATH - UCL BSM structural classification of proteins
  • SCOP - Structural classification of proteins [Mirrors]
  • HCA - Hydrophobic Cluster Database
  • Molecules To Go - Molecules To Go (formerly known as Molecules R Us), browser for PDB
  • BMM Domain Fishing - Biomolecular Modelling Laboratory (ICRF) protein domain fishing
  • Relibase - Receptor/ligand complexes db [Mirror in USA]
  • CCDC - Cambridge Crystallographic Data Center (Cambridge Structural Db (CSD))
  • HSSP - Homology-derived secondary structure of proteins db
  • MutaProt - Comparison of PDB files which differ by point mutations
  • DisProt - Database of Protein Disorder
  • SWISS-3DIMAGE SIB logo - 3D images of proteins and other biological macromolecules
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Proteomics databases and links
Gel-based data
Mass spectrometry data
  • GPMdb - Global Proteome Machine Database
  • OPD - Open Proteomics Database (currently down)
  • PeptideAtlas - peptides identified in tandem mass spectrometry proteomics experiments
  • PRIDE - PRoteomics IDEntifications database
  • Tranche - Peer-to-peer distributed file system
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Nucleotide and related 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)
  • Ensembl - Genome database for vertebrates and other eukaryotic species
  • UCSC Genome Browser
  • AsDb - Aberrant Splicing db
  • ACUTS - Ancient conserved untranslated DNA sequences db
  • Codon Usage Db
  • EPD SIB logo - Eukaryotic Promoter db
  • HOVERGEN - Homologous Vertebrate Genes db
  • IMGT - ImMunoGeneTics db [Mirror at EBI]
  • RDP - Ribosomal db Project
  • PLACE - Plant cis-acting regulatory DNA elements db
  • PlantCARE - Plant cis-acting regulatory DNA elements db
  • smiRNAdb SIB logo - Information about mammalian small RNAs
  • ssu rRNA - Small ribosomal subunit at the European ribosomal RNA database
  • lsu rRNA - Large ribosomal subunit at the European ribosomal RNA database
  • 5S rRNA - 5S ribosomal RNA db
  • greengenes - 16S rRNA gene database and workbench
  • tmRNA Website
  • tmRDB - tmRNA dB
  • tRNA - tRNA compilation from the University of Bayreuth
  • RNA editing - RNA editing site
  • RNAmod db - RNA modification db
  • MPDB - Molecular probe db
  • VectorDB - Vector sequence db
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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
  • 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
  • DSDBASE - Disulfide database (derived from 3D data)
  • GlycoSuiteDB SIB logo - Db of glycan structures
  • LIPID MAPS - LIPID Metabolites And Pathways Strategy
  • GlycateBase - Database of glycation data for epsilon amino groups of lysines
  • O-GlycBase - O-glycosylated proteins db
  • Phospho.ELM - Phosphorylation sites db
  • PhosphoSite - Db of phosphorylation sites in human and mouse proteomes
  • DOLOP Db of bacterial lipoproteins
  • UbiProt - Db of ubiquitylated proteins
  • RESID - Db of Amino Acid Modifications
  • Delta Mass - Db of mass of Post-Translational Modifications
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Phylogenetics and taxonomy databases & resources
  • COG and KOG - Phylogenetic classification of proteins encoded in complete genomes
  • eggNog - Automated construction and annotation of orthologous groups of genes
  • EGO - Eukaryotic Gene Orthologs
  • Ensembl Compara - Genome-wide species comparisons
  • HOGENOM - Homologous Sequences in Complete Genomes Database
  • HOVERGEN - Homologous Vertebrate Genes Database
  • InParanoid - Eukaryotic ortholog groups
  • KO - KEGG Orthology:
  • Metazome - Phylogenomic analysis of metazoan gene families
  • Optic - Orthologous and paralogous transcripts in clades
  • OMA - Orthologs Matrix Project (OMA)
  • OrthoDB Hierarchical catalog of eukaryotic orthologs
  • OrthoMCL DB Ortholog grouping for protein sequences from multiple genomes
  • PhylomeDB - Database for phylomes (collections of phylogenetic trees for all proteins encoded in a given genome)
  • P-POD - Princeton Protein Orthology Database with an emphasis on providing information about disease-related genes
  • Protein Clusters - NCBI collection of related protein sequences (clusters)
  • PhyloFacts - Pre-calculated structural and phylogenomic analyses of protein families and domains
  • TreeFam - Tree families database of phylogenetic trees of animal genes
  • CluSTr - Automatic classification of UniProtKB proteins into groups of related proteins
  • HomoloGene - Automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes
  • ProtoNet - Classification of the proteins into hierarchical clusters
  • NCBI Taxonomy Browser
  • Taxonomy - UniProt Taxonomy Browser
  • The Tree of life - Collection of WWW pages on phylogeny and biodiversity of organisms
  • TreeBASE - Relational db of phylogenetic information
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Gene expression databases and resources
  • 4DXpress - a database for cross-species expression pattern comparisons
  • ArrayExpress - MicroArray informatics at the EBI
  • Bgee SIB logo - Retrieve and compare gene expression patterns across species
  • BioGPS - The Gene Portal Hub
  • CleanEx SIB logo - database of gene expression profiles
  • ExpressDB - Yeast and E.coli RNA expression db
  • GeneX - An open source Gene Expression database
  • GEO - Gene Expression Omnibus
  • GXD - MGI Gene Expression Database (mouse)
  • RAD - RNA abundance db
  • SMD - Stanford microarray db
  • MILANO - Microarray Literature-based Annotation
  • Genevestigator - a multi-organism, novel type of online meta-analysis tool for gene expression
  • GEMLeR - Gene Expression Machine Learning Repository
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Patents databases
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References (bibliographic databases)
  • PubMed Medline server
  • BioMedSearch - an enhanced version of the NIH PubMed/MedLine search
  • AGRICOLA - AGRICultural OnLine Access; ref. db from NAL
  • RefDoc (ex-Article@INIST) - Scientific and Technical Information Institute articles and monographs db
  • SeqAnalRef - Sequence analysis bibliographic references
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Dictionaries, protocols, courses, nomenclature, etc.
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Biological software and databases catalog servers
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Gateways (portals) to Life Science resources
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Biological journals and publishers
Resources linking 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
  • ATC-LGCC - American Type Culture Collection
  • Biochemical Society
  • BSA - Botanical Society of America
  • CSBMCB - Canadian Society of Biochemistry and Molecular and Cell Biology
  • EFBF - European Federation of Biophysics
  • 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
  • HUGO - HUman Genome Organization
  • HUPO - HUman Proteome Organization
  • IUBMB - International Union of Biochemistry and Molecular Biology
  • IUPAC - International Union of Pure and Applied Chemistry
  • 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
  • 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 SIB logo - Swiss Institute of Bioinformatics
  • EMBnet CH SIB logo - Switzerland EMBnet node
  • ISREC SIB logo - ISREC/SIB Computational Cancer Genomics group (Lausanne / Switzerland)
  • CBRG - Computational Biochemistry Research Group (Zurich / Switzerland)
  • ABIM - Atelier BioInformatique (Marseille / FR)
  • B3E - Bioinformatique/Biostatistique/Biomathematique/Epidemiologie (Paris / FR)
  • 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)
  • IMPBIO - Informatique, Mathématiques, Physique en Biologie moléculaire
  • Pasteur - Institut Pasteur (Paris / FR)
  • PBIL - Pole Bio-informatique Lyonnais (Lyon / FR)
  • Sanger - Sanger Centre (Hinxton / U.K.)
  • BMM - Biomolecular Modelling laboratory at ICRF (London / U.K.)
  • BSM - Biomolecular Structure and Modelling group at UCL (London / U.K.)
  • Manchester - Manchester University Bioinformatics unit (U.K.)
  • HUSAR - Biocomputing Service at DKFZ
  • AG BIODV - Software Development for Molecular Biology at Helmholtz Zentrum (Germany)
  • FLI - Genome Analysis in Complex Diseases, Ageing and Model Organisms (Germany)
  • MDC:Bioinf - Department of Bionformatic of the Max Delbruck Center for Molecular Medicine (Germany)
  • MIPS - Munich Information Centre for Protein Sequences (Germany)
  • PZR - Bioinformatics at the Proteome Center Rostock (Germany)
  • BEN - Belgium EMBnet node
  • CBS - Center for Biological Sequence Analysis (Technical University of Denmark)
  • CSC BioBox - Resources for Bioscientists
  • ABC - Agricultural Biotechnology Center (Budapest / Hungary)
  • Telethon Italy
  • CMBI - Center for Molecular and Biomolecular Bioinformatics; Netherland EMBnet node
  • BIO - Biotechnology Centre of Oslo; Norway EMBnet node
  • IBB - Institute of Biochemistry and Biophysics (Warsaw); Poland EMBnet node
  • IGC - Bioinformatics and Computational Unit of the Instituto Gulbenkian de Ciencia; Portugal EMBnet Node
  • Belozersky Institute - GeneBee Molecular Biology server (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 Computer
  • LCB - Linnaeus Centre for Bioinformatics
  • SBC - Stockholm Bioinformatics Center
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 - Life Sciences Resources and Reference Tools
  • Biotechnology - National Agricultural Library - Biotechnology
  • BMERC - Biomolecular Engineering Research Center
  • BROAD Institute
  • CBIL - Computational Biology and Informatics Laboratory at the University of Pennsylvania
  • CCB - Washington University Center for Computational Biology
  • CUBIC - Columbia University Bioinformatics Center / RostLab
  • JCVI - J. Craig Venter Institute
  • JGI - Doe Joint Genome Institute
  • NCGR - National Center for Genome Resources
  • NIH - Computational Molecular Biology at NIH
  • UCLA - UCLA Bioinformatics Institute
  • Bioinformatics & Research Computing at Whitehead Institute
  • CCB - Centre for Computational Biology at the Hospital for sick children
Asia
  • APBioNet - Asia-Pacific Bioinformatics network
  • BIDD - Bioinformatics & Drug Design group (National University / Singapore)
  • DIC - Bioinformatics Centre at the University of Pune
  • 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)
  • MGRC - Malaysian Genomics Resource Centre
  • 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 Genomic Interactions 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
  • 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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Other links

Miscellaneous medical references sites
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Miscellaneous scientific references sites

Disclaimer

This list is not supposed to be complete, it will list servers that we find useful and up-to-date.
Last modified 21/OCT/2010 by GGR