PIPSA may be used to compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins. It is described in detail in:

N. Blomberg, R.R. Gabdoulline, M. Nilges and R. C. Wade.
Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.
Proteins: Str., Function and Genetics, 37:379-387 (1999).

The interaction properties are computed from the 3D coordinates of the set of superimposed proteins.
Similarity indices can be computed and analysed for three different types of property:
    1.  The monopole and dipole moments of proteins, which are analytically computed descriptors for their electrostatic potentials;
    2.  Electrostatic potentials obtained by numerically solving the finite-difference Poisson-Boltzmann equation (FDPBE) on a grid;
    3.  Other types of interaction property, e.g. probe interaction energies evaluated with the GRID program, that can be mapped on to a grid.
PIPSA produces a matrix of pairwise similarity indices for each protein interaction property. This matrix is converted into a distance matrix which may  be used for clustering or visualization.

Requirements for running PIPSA:

    1. Coordinates for the superimposed set of proteins  to be analyzed.    2.  Additional licensed programs may be required, depending on the type of the similarity calculation performed.        All necessary auxiliary data files and scripts for running these programs are provided.

Availability:

   Currently the version 2.0 of PIPSA is available. Here is PIPSA 2.0 page.