PIPSA tool page EML Research Home

webPIPSA

Protein Interaction Property Similarity Analysis

New features (Spring 2009)

The following new features are now available (see also feature history):
  • Upload of PQR files for protein structures: So far protein structures were either modelled (using the workflow starting with the Uniprot accession code) or uploaded in PDB format. The advantage of uploading PQR files is that with this format nonstandard atom types for the calculation of electrostatic potentials can be supported. Atoms with non standard atom types are removed from PDB files (see the output of the webserver).
  • Selection of multiple templates to investigate the influence of protein flexibility conformational variability. Sometimes more than one structure is available for a protein. To assess the effects of using different conformations for the template, the modelling step in the workflow starting with Uniprot accession codes allows now the selection of several templates. Each sequence is modelled against all selected templates and, after comparison of all models, the resulting comparison matrix is presented (see example).
  • A demonstration/tutorial for performing an analysis for relating kinetic constannts to PIPSA data is given.

Introduction

This PIPSA service is provided for the comparison of the electrostatic interaction properties of proteins. It permits the classification of proteins according to their interaction properties. PIPSA may assist in function assignment, the estimation of binding properties and enzyme kinetic parameters. See References for details.

Method

To perform PIPSA on this webserver, you need to upload a set of related protein structures in PDB format. After calculation of the protein electrostatic potentials, the server will calculate similarity indices for all pairs of proteins based on the electrostatic similarity. These indices will be computed for complete protein 'skins' or for a user defined region. The similarity indices are then converted to electrostatic 'distances'. The electrostatic potential distance matrix is displayed in color coded form (heat map) and as a tree (epogram).

Start a PIPSA analysis (input PDB format coordinate files).

Start a PIPSA analysis (input SWISSPROT entries with EC annotation)*.

* This type of analysis involves a protein structural modelling step utilizing Modeller. Therefore this part is subject to the Modeller license conditions. Please obtain a Modeller license to use this service.