Benchmarking of dimeric threading and structure refinement.

The understanding of protein-protein interactions is a major goal in the postgenomic era. The prediction of interaction from sequence and the subsequent generation of full-length dimeric models is therefore of great interest especially because the number of structurally characterized protein-protein complexes is sparse. A quality assessment of a benchmark comprised of 170 weakly homologous dimeric target-template pairs is presented. They are predicted in a two-step method, similar to the previously described MULTIPROSPECTOR algorithm: each target sequence is assigned to a monomeric template structure by threading; then, those templates that belong to the same physically interacting dimer template are selected. Additionally we use structural alignments as the "gold standard" to assess the percentage of correctly assigned monomer and dimer templates and to evaluate the threading results with a focus on the quality of the alignments in the interfacial region. This work aims to give a quantitative picture of the quality of dimeric threading. Except for one, all monomer templates are identified correctly, but approximately 40% of the dimer templates are still problematic or incorrect. Preliminary results for three full-length dimeric models generated with the TASSER method show on average a significant improvement of the final model over the initial template.

Making sense of big data in health research: Towards an EU action plan.

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans.

Prediction of physical protein-protein interactions.

Many essential cellular processes such as signal transduction, transport, cellular motion and most regulatory mechanisms are mediated by protein-protein interactions. In recent years, new experimental techniques have been developed to discover the protein-protein interaction networks of several organisms. However, the accuracy and coverage of these techniques have proven to be limited, and computational approaches remain essential both to assist in the design and validation of experimental studies and for the prediction of interaction partners and detailed structures of protein complexes. Here, we provide a critical overview of existing structure-independent and structure-based computational methods. Although these techniques have significantly advanced in the past few years, we find that most of them are still in their infancy. We also provide an overview of experimental techniques for the detection of protein-protein interactions. Although the developments are promising, false positive and false negative results are common, and reliable detection is possible only by taking a consensus of different experimental approaches. The shortcomings of experimental techniques affect both the further development and the fair evaluation of computational prediction methods. For an adequate comparative evaluation of prediction and high-throughput experimental methods, an appropriately large benchmark set of biophysically characterized protein complexes would be needed, but is sorely lacking.