Editorial

In our days, there is an explosion on the use of Topological Indices (TIs) and Connectivity Indices (CIs) described from graph theory to study Complex Networks on a broad spectrum of topics related to Bioinformatics and Proteomics. These topics cover many biomedical fields from Virology, Parasitology, and Microbiology in general to Toxicology, and Cancer research to cite only some of the more investigated. The main reason for this success of TIs/CIs, is the high flexibility of this theory to solve in a fast but rigorous way many apparently unrelated problems in all these disciplines. This determined the recent development of several interesting software and theoretical methods to handle with structure-function information and data mining in this field. In a recent, preliminary review in the field Gonzalez-Diaz H et al. Proteomics (2008) 8, 750-778, we noted that these software and methods may work at different structural levels including: -structure of protein ligand drugs, -protein structure, -protein-protein, protein-DNA and other types of protein involving interactions. -protein mediated cell-to-cell or organism-organism interactions. -numerical description of 2D electrophoretic proteomics maps. -prediction of protein fragmentation connected to mass spectra. -numerical description of whole blood proteome Mass Spectra and other topics. In any case, in only one manuscript is very difficult to zip all this information. So it is necessary a topic issue because many of the users of these programs limit to a narrow field of application and ignore the several applications at different proteomics levels. On the other hand, many researchers, which move by the frontiers of these fields, miss a journal issue reviewing the actual applications and future perspectives of these software and methods and the possible relationships of data flow between them in a common theoretic framework. Such a collection of papers could be of the major interest for many specialists on proteomics and may increase the interchange between these specialists of different but related fields with a common root: proteomics and graph theory. In addition, it could be the seed for further improvement of software performance and compatibility. Taking into consideration all these aspects, Current Proteomics presents this special issue composed by a collection of papers devoted to review the common theoretic basis, applications, and inter-connections between the inputs and outputs of some of the more used Cheminformatics-Bioinformatics and Data Mining software or methods (about one paper per method) that enable calculation of TIs and their applications to Proteomics. We hope that the present issue may serve as a bridge between theoretical scientists in graph theory and experimentalists in proteomics in order to suggest new areas of mutual interchange and collaboration.