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Tools for the analysis of protein sequences and models
Task Server / Data base
Find protein sequence
  • search e.g. for "hen egg and lysozyme"
  • check annotations concerning literature, 3D structure (PDB code?), etc.
    		•  Expasy
      search by keywords  (e.g. for "hen egg and lysozyme)
      search by accession number or ID (e.g. LYC_CHICK)

    Statistical analysis of protein sequence     		SAPS

    Intrinsic disorder     		DisEmbl GlobPlot

    Predict secondary structure     		GORIV (Attention the program uses a 17-residue window!)
    NeuronalNetworkPredict
    PredictProtein  (requires e-mail)
    SOPM
    PSIPRED
    Search for homologuous sequences BLAST (with CLUSTALW interface)
    Sequence alignment SIM (for 2 sequences)
    CLUSTALW (multiple sequences)
    Structure based sequence alignment Overview 1
    Overview 2 (wiki)
    topmatch (Sippl)
    Expresso (align sequence to a structure with a homolog sequence)
    Mammoth (multiple structure alignment)
    SSM (best!)
    Predict transmembrane helices TMHMM
    DAS
    Is there a homologous protein with known structure? SwissModel  (click Search in left menu)
    Examine a 3D structure
    retrieve structure by specifing the PDB code (if known) or use "SearchLite"
    		PDB (www.pdb.org)
    • after having found the structure, use "Sequence details" to get quick overview about 2nd structure
    • have a look! (View Structure / FirstGlance)

      • or
    • download the structure (uncompressed, PDB format) and examine it with Swiss-PDBViewer (installed locally)

     
    Other tools and databases
    Entry to Expasy tools proteomics tools
    Predict coiled-coil structures  COILS
    Data base of homologous domains HOMSTRAD
    Predict transmembrane b-strands Kay's programme (not the best)
    metaserver
    B. Rost overview article (also for a-helical proteins)
    PRED-TMBB
    PROFtmb (pretty nice)
    Literature
    (also good database for references to sequences and structures)     		Entrez
    (straight-forward search like "myoglobin and whale")
    Course on Protein Structures Protein Structure Tutorial
    Postscript of alignment ESPript
    updated 30.06.2008 TS