Nicholas J. Schisler, PhD


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 | Misc. medical ref. sites | Misc. scientific ref. sites |

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) [Mirrors at St. Louis (USA), Sanger Institute, UK, Karolinska Institutet (Sweden)]
  • 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 Database
  • DIP - Database of Interacting Proteins
  • MINT - Molecular INTeraction database
  • HPRD - Human Protein Reference Database
  • IntAct
  • GRID - General Repository for Interaction Dataset
  • PPI - JCB Protein-Protein Interaction Website
  • PID - MRC Protein Interaction Databases

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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]
  • Molecules To Go - Molecules To Go (formerly known as Molecules R Us), browser for PDB
  • BMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server
  • 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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Proteomics databases and links

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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)

     

  • 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
  • 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
  • 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
  • TelDB - Multimedia Telomere Resource

     

  • MPDB - Molecular 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 gen

     

  • 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

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Microarray databases and resources

  • ArrayExpress - MicroArray informatics at the EBI
  • ExpressDB - Yeast and E.coli RNA expression db
  • GeneX - Gene Expression project
  • GEO - Gene Expression Omnibus
  • RAD - RNA abundance db
  • SMD - Stanford microarray db

     

  • MILANO - Microarray Literature-based Annotation

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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)
  • Freepatentsonline - access to millions of patents

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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
  • 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 - 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)
  • 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)
  • EGOISt -Master professionnel de BioInforMatique de l'Universit de Rouen

     

  • 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.)
  • 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)
  • PZR - Bioinformatics at the Proteome Center Rostock
  • 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
  • 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 - 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
  • 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
  • IBC - Washington University Institute for Biomedical Computing
  • JGI - Doe Joint Genome Institute
  • 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)

     

  • 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

  • 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
  • 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
  • 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

     

  • Electronic Orange Book - FDA list of approved drug products

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Miscellaneous scientific references sites

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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 | Misc. medical ref. sites | Misc. scientific ref. sites |

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Send mail to nicholas.schisler@furman.edu with questions or comments about this web site.
Copyright © 1997-2005 Nicholas Schisler, PhD
Last modified: June 10, 2005

Links of this page are taken from ExPASy Life Sciences Directory Release March 22, 2005: http://us.expasy.org/links.html