Author(s): Idowu OC, Lynden SJ, Periorellis P, Young MP, Andras P
Abstract: The process of rational drug discovery requires analysis of complex biological systems such as protein-protein interaction, metabolic pathways and gene interaction networks. Our aim is to develop a software suite for data retrieval and analysis that can aid in protein target detection in the context of rational drug design. The software suite is divided into four key modules: data retrieval and integration, data analysis, data visualisation and data presentation. Data retrieval and integration involves automating the process of extracting interaction data from public database sources such as Database of Interacting Proteins (DIP), Kyoto Encyclopaedia of Genes and Genomes (KEGG), published journal articles, and protein sequence databases such as Swiss-Prot. Data obtained from different sources are integrated into a common data format and are archived as a single data source for various species. Data analysis involves predicting functional protein targets for drug discovery using different statistical and graph theoretic tools. Targets are selected by identifying proteins that significantly compromise the structural integrity of a parasite protein network with minimal damage to the host organism. Network structures are visualised using topologically force-directed layout algorithms, with a graphical user interface which allows the user to visualise the properties of the protein targets identified by the algorithms, and the effects of their removal on the network structure. Furthermore the software offers facilities for data presentation in terms of textual report and interactive charts of network analysis.
Keywords: rational drug discovery, protein-protein interactions, proteomics