Computational Biochemistry Group

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  • Some Databases/Servers

  • NCBI: The National Center for Biotechnology Information
  • EBI: The European Bioinformatics Institute
  • DDBJ: DNA Data Bank of Japan
  • KEGG: Kyoto Encyclopedia of Genes and Genomes
  • Brenda

  • NAR -- Database Collection
  • NAR -- Webserver Collection

  • Protein Data Bank
  • WebCSD (Cambridge Structural Database)
  • Crystallography Open Database

  • Orientations of Proteins in Membranes
  • Heme Protein Database
  • eQuilibrator -- thermodynamic analysis of biochemical systems
  • Phyre2 -- Protein Structure Prediction
  • BackPhyre -- Protein Structure Prediction

  • pKa values and BDE server -- iBonD

  • SignalP
  • TermiNator-Terminal Editing (like N-terminal methionine excision)



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  • CCL: Computational Chemistry List



  • Python Related Science

    • Python
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    • Biopython
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    • PyQuante: Python Quantum Chemistry
    • cclib -- Interpreting the results of computational chemistry packages
    • matplotlib
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    • Pdynamo
    • GTKDynamo
    • Computational Crystallography Toolbox
    • NMRGlue
    • IPython -- User Interface
    • BPython -- UserInterface
    AG Ullmann