Existing protein-protein interactions databases cover only a portion of the interactome and interaction information on protein isoforms is underrepresented. This leads to a lack of information on the functional similarity of protein isoforms and the effects of transcript diversity on the protein interaction networks. We present a comprehensive automated literature analysis that extracts interactions involving human protein isoforms linked to clusters of transcripts with high sequence similarity and deliver them in a database called TBIID for knowledge discovery. We measure the interaction variability of the isoforms from the clustered transcripts by analysing the distribution of their interaction partners in TBIID. Almost all clusters analyzed (99%) contain isoforms with unique partners indicating that isoforms are specialized towards forming unique interactions and thus achieving functional diversity, which is similar to the results from public resources. TBIID is available at http://tbiid.emu.edu.tr containing most relevant candidates for future experiments focusing on understanding the isoform interaction networks and the resulting functional implications.

written by Journal of Proteomics and Bioinformatics

This article introduces some of the recent developments in drug re-profiling with emphasis on how computational chemistry and biology approaches together with access to public data bases can help generate new leads from existing drugs. It discusses the drawbacks of high-throughput (HTS) genomics and how the concepts of target polypharmacology can help speed up delivery of the next generation of drugs. Some of the successful strategies for drug re-profiling are presented and computational tools are discussed.

written by Journal of Proteomics and Bioinformatics

The practice of epilepsy surgery has largely shifted from invasive investigations with chronic intracranial electrodes to high resolution imaging modalities that may delineate the epileptogenic zone in a non-invasive manner. Nevertheless, non-lesional cases, particularly due to extratemporal cryptic pathology, still pose a major challenge. Here we describe the value of combining traditional electrocorticography with the innovation of 7 Tesla magnetic resonance imaging for the detection of a focal cortical dysplasia and thereby sparing the need for further invasive investigation with chronic intracranial electrodes. We conclude that, especially for extratemporal malformations of cortical development, the use of electrocorticography guided by higher resolution magnetic resonance imaging may effectively delineate the epileptogenic zone and define appropriate resection margins. This highlights the importance of a multidisciplinary approach and of combined neurophysiologic and imaging techniques in contemporary epilepsy surgery.

written by Journal of Neurology and Neurophysiology