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Available from: Michele Vendruscolo, Dec 19, 2014
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    ABSTRACT: NMR chemical shifts are sensitive probes of structure and dynamics in proteins. Empirical models, based on a large database of measured shifts, take an input structure and provide increasingly accurate estimates of the corresponding shifts. Quantum chemical calculations can provide the same information, with greater generality but (currently) with less accuracy. These methods are now providing new ways to approach NMR structure determination, and new insights into the conformational dynamics of proteins.
    No preview · Article · Feb 2013 · Current Opinion in Structural Biology
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    ABSTRACT: An efficient method to extract and store information from NMR spectra is proposed that is suitable for comparison and construction of a search engine. This method based on trees doesn't require any peak picking or any pre-treatment of the data and is found to outperform the currently available methods, both in terms of compactness and velocity. Our approach was tested for 1D proton spectra and 2D HSQC spectra and compared with the method proposed by Pretsch and coworkers and [Bodis et al. 2007, Bodis et al. 2009]. Additionally, the correspondence between spectral and structural similarity was evaluated for both methods.
    Full-text · Article · Aug 2013 · Chemometrics and Intelligent Laboratory Systems
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    ABSTRACT: Reactive oxygen species (ROS)-mediated dysfunction of certain biological processes is implicated in different diseases in humans, including cardiovascular, cancer, or neurodegenerative disorders. Not only human cells and tissues are affected by ROS but also all other biological systems, including plants and microorganisms. Primary targets of ROS are proteins, lipids, and nucleic acids. Modifications of these macromolecules result mostly in the start of signalling cascades between proteins, proteins and DNA, DNA and RNA, proteins and RNA, proteins and lipids within single cell compartments, entire cells, or tissues. In this chapter, basics of tools of structural biology (i.e., X-ray crystallography, NMR, and EPR spectroscopy) as well as bioinformatics are presented. These tools are explained as well as how they can be applied in the analysis of ROS-mediated modifications within macromolecules and systems, and perspectives are discussed.
    Full-text · Chapter · Jun 2014
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