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Protein Interaction Property Similarity Analysis

This demonstration consists of two demonstrations:

  1. Part 1:
  2. Part 2:

qPIPSA: Relating enzymatic kinetic parameters and interaction fields. Razif R Gabdoulline, Matthias Stein and Rebecca C Wade BMC Bioinformatics 2007, 8:373 (fulltext)

Demonstration example

This dataset consists of the modelled structures of Triosephosphate isomerases (TPI) from different species as described in the following publication: Part 1: To run this example, do the following: The result will be displayed as an image (as below) relating the TPI enzymes of the different species according to electrostatic similarity.

The distances calculated from the similarity indices for the electrostatic potentials are shown in a color coded matrix view (heat map). Red/orange colors indicate similar potentials, whereas blue color marks proteins with more distant electrostatic potentials.

The tree along the side of the image group the proteins into groups of similar electrostatic potentials.

Part 2 for relating kinetic data:

This example shows, how the qPIPSA approach can assist in the validation as well as estimation of kinetic parameters.