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