1) Swiss Institute of Bioinformatics

ExPASy (Expert Protein Analysis System) Tools
(the tools can be accessed by category or by resources A-Z)  

  • Sequence Alignment tools
    - BLAST (BLASTp)
  • ENZYME (repository of information relative to the nomenclature of enzymes)
  • Compute pI/MW and ProtParam (calculate pI, % composition, e280nm, etc)
    - HelixWheel (this is no longer on the ExPASy site, use Helical Wheel)
  • Secondary
    ProtScale - allows you to compute and represent the profile produced by any
    amino acid scale on a selected protein. For instance, you can enter the Accession
    number for a protein and predict the secondary structure content based on the
    amino acid sequence using Chou-Fasman parameters.
    -----Use the following Excel file to assist in the prediction of secondary structure using Chou-Fasman parameters
    ----- Compare the actual secondary structure of Goose Lysozyme to that prediced using Chou-Fasman parameters within ProtScale
  • Tertiary structure analysis tools - http://expasy.org/structural_bioinformatics

2) European Bioinformatics Institute

Tools for Multiple and pairwise protein stuctural comparison and sequence alignment