BACKGROUND: Protein-protein interactions can be considered the basic skeleton 
for living organism self-organization and homeostasis. Impressive quantities of 
experimental data are being obtained and computational tools are essential to 
integrate and to organize this information. This paper presents Protopia, a 
biological tool that offers a way of searching for proteins and their 
interactions in different Protein Interaction Web Databases, as a part of a 
multidisciplinary initiative of our institution for the integration of 
biological data http://asp.uma.es.
RESULTS: The tool accesses the different Databases (at present, the free version 
of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with 
biological protein names or databases codes and can be depicted as a vector or a 
matrix. They can be represented and handled interactively as an organic graph. 
Comparison among databases is carried out using the Uniprot codes annotated for 
each protein.
CONCLUSION: The tool locates and integrates the current information stored in 
the aforementioned databases, and redundancies among them are detected. Results 
are compatible with the most important network analysers, so that they can be 
compared and analysed by other world-wide known tools and platforms. The 
visualization possibilities help to attain this goal and they are especially 
interesting for handling multiple-step or complex networks.