Protopia: a protein-protein interaction tool.
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.


CONCLUSIONS
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.
Real-Chicharro
Alejandro
A
University of Malaga and CIBER de Enfermedades Raras, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Instituto de Salud Carlos III, Spain. areal@lcc.uma.es
Ruiz-Mostazo
Iván
I
Navas-Delgado
Ismael
I
Kerzazi
Amine
A
Chniber
Othmane
O
Sánchez-Jiménez
Francisca
F
Medina
Miguel Angel
MA
Aldana-Montes
José F
JF
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
D011506:Proteins