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Protein related databases

  • UniProt - the universal protein resource
  • UniProt Knowledgebase - consists of UniProtKB/Swiss-Prot (high-level annotation) and UniProtKB/TrEMBL (computer-annotated)
  • PMD - Protein Mutant db

  • InterPro - Integrated Resources of Proteins Domains and Functional Sites
  • PROSITE - 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)
  • PROTOMAP - An automatic hierarchical classification of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL proteins
  • 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



Protein 3D structure related databases

  • PDB - Protein Data Bank
  • PDBTM - Protein Data Bank of Transmembrane Proteinsnew
  • 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 [ 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]
  • 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
  • DisProt - Database of Protein Disorder

  • SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
  • BioImage - Biological image db (contains imaging data on macromolecules)



Proteomics databases and links

Gel-based data
Mass spectrometry data
  • GPMdb - Global Proteome Machine Database
  • OPD - Open Proteomics Database
  • PeptideAtlas - peptides identified in tandem mass spectrometry proteomics experiments
  • PRIDE - PRoteomics IDEntifications database
  • Tranche - Peer-to-peer distributed file system



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 - 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 - 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



Carbohydrates resources



Species specific databases:

Human
Vertebrates
Mitochondrion and chloroplast
  • GOBASE - Organelle Genome Database
  • MitoDat - Mendelian Inheritance and the Mitochondrion db (mitochondrial nuclear gen

  • C.caldarium - Cyanidium caldarium strain RK1 chloroplast genome
Insects
Invertebrates
Plants
Fungi
Bacteria
Archaea
Viruses and phages



Human mutation databases/resources



Gene(s)/protein(s) specific databases/resources



Post-translational modifications databases and resources

  • DSDBASE - Disulfide database (derived from 3D data)
  • GlycoSuiteDB - 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
  • Phosphorylation site db - Bacterial and archaeal phosphorylation sites resource
  • 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



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 Vetebrate 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
  • NEWT - UniProt Taxonomy Browser
  • The Tree of life - Collection of WWW pages on phylogeny and biodiversity of organisms
  • TreeBASE - Relational db of phylogenetic information



Gene expression databases and resources

  • 4DXpress - a database for cross-species expression pattern comparisons
  • ArrayExpress - MicroArray informatics at the EBI
  • Bgee SIB - Retrieve and compare gene expression patterns across species
  • BioGPS - The Gene Portal Hubnew
  • CleanEx SIB - 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)new
  • 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 Repositorynew



Patents databases



References (bibliographic databases)



Dictionaries, protocols, courses, nomenclature, etc.



Biological software and databases catalog servers



Gateways (portals) to Life Science resources



Biological journals and publishers

Resources linking to journals home pages
Publishers
Bioinformatics journals and newsletters
Genomic newsletters
Miscellaneous
Biotechnology trade journals
General science journals



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



Biocomputing servers homepages

Europe
  • EBI - European Bioinformatics Institute
  • EMBnet - European Molecular Biology Network
  • EMBL - EMBL Biocomputing unit

  • SIB SIB - Swiss Institute of Bioinformatics
  • EMBnet CH SIB - Switzerland EMBnet node
  • ISREC SIB - ISREC/SIB Computational Cancer Genomics group (Lausanne / Swizerland)
  • 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.)
  • RIO - Roslin Institute Online (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)
  • VSNS BCD - Virtual School of Natural Sciences Biocomputing Division from the University of Bielefeld (Germany)

  • BEN - Belgium EMBnet node
  • CBS - Center for Biological Sequence Analysis (Technical University of Denmark)
  • CSC BioBox - CSC; Finland EMBnet node
  • 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

  • CBR - Canadian Bioinformatics Resource (currently not working)
  • CCB - Centre for Computational Biology at the Hospital for sick children
Asia
  • APBioNet - Asia-Pacific Bioinformatics network

  • BIC-JNU - Bioinformatics Center of Jawaharlal Nehru University
  • 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

  • BDT - Base de Datos Tropical (Sao Paulo / Brazil)

  • ICGEB - International Center for Genetic Engineering and Biotechnology (Trieste / Italy)



Biotechnology and pharmaceutical companies



Bioinformatics companies




Other links

Miscellaneous medical references sites


Miscellaneous scientific references sites



Websites with Useful links:


NCBI Resource Guide

Bioinformatics Links Directory

Bioinformatics Links

Bioinformatics Resources

World of Bioinformatics Links






 


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