PIPSA (Protein Interaction Property Similarity Analysis)

    


Version 3.0, January 2008
R. R. Gabdoulline,  R.C. Wade,

EML Research, Heidelberg, Germany
EMBL, Heidelberg, Germany


New:   webPIPSA - PIPSA web server

PIPSA may be used to compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins.

It is first described 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 a 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.


Theoretical Introduction

Short Overview

Installation

User Guide

Usage example

Application examples

Versions and availability

References

FAQ