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Maurer-Stroh S.,Agency for Science and Technology A STAR | Maurer-Stroh S.,Nanyang Technological University | Gao H.,Agency for Science and Technology A STAR | Gao H.,National University of Singapore | And 8 more authors.
Journal of Bioinformatics and Computational Biology | Year: 2013

Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif-structural motif-function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions. Many of these, so called zinc fingers, are structurally independent globular domains with discontinuous binding motifs made up of residues mostly far apart in sequence. Through a systematic approach starting from the BRIX structure fragment database, we discovered that there exists another predictable subset of zinc-binding motifs that not only have a conserved continuous sequence pattern but also share a characteristic local conformation, despite being included in totally different overall folds. While this does not allow general prediction of all Zn binding motifs, a HMM-based web server, Huf-Zinc, is available for prediction of these novel, as well as conventional, zinc finger motifs in protein sequences. The Huf-Zinc webserver can be freely accessed through this URL (). © 2013 Imperial College Press.

Agency: GTR | Branch: EPSRC | Program: | Phase: Training Grant | Award Amount: 3.94M | Year: 2014

The achievements of modern research and their rapid progress from theory to application are increasingly underpinned by computation. Computational approaches are often hailed as a new third pillar of science - in addition to empirical and theoretical work. While its breadth makes computation almost as ubiquitous as mathematics as a key tool in science and engineering, it is a much younger discipline and stands to benefit enormously from building increased capacity and increased efforts towards integration, standardization, and professionalism. The development of new ideas and techniques in computing is extremely rapid, the progress enabled by these breakthroughs is enormous, and their impact on society is substantial: modern technologies ranging from the Airbus 380, MRI scans and smartphone CPUs could not have been developed without computer simulation; progress on major scientific questions from climate change to astronomy are driven by the results from computational models; major investment decisions are underwritten by computational modelling. Furthermore, simulation modelling is emerging as a key tool within domains experiencing a data revolution such as biomedicine and finance. This progress has been enabled through the rapid increase of computational power, and was based in the past on an increased rate at which computing instructions in the processor can be carried out. However, this clock rate cannot be increased much further and in recent computational architectures (such as GPU, Intel Phi) additional computational power is now provided through having (of the order of) hundreds of computational cores in the same unit. This opens up potential for new order of magnitude performance improvements but requires additional specialist training in parallel programming and computational methods to be able to tap into and exploit this opportunity. Computational advances are enabled by new hardware, and innovations in algorithms, numerical methods and simulation techniques, and application of best practice in scientific computational modelling. The most effective progress and highest impact can be obtained by combining, linking and simultaneously exploiting step changes in hardware, software, methods and skills. However, good computational science training is scarce, especially at post-graduate level. The Centre for Doctoral Training in Next Generation Computational Modelling will develop 55+ graduate students to address this skills gap. Trained as future leaders in Computational Modelling, they will form the core of a community of computational modellers crossing disciplinary boundaries, constantly working to transfer the latest computational advances to related fields. By tackling cutting-edge research from fields such as Computational Engineering, Advanced Materials, Autonomous Systems and Health, whilst communicating their advances and working together with a world-leading group of academic and industrial computational modellers, the students will be perfectly equipped to drive advanced computing over the coming decades.

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