Biochemistry and Pharmacology - Research Publications

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    Scipion web tools: Easy to use cryo-EM image processing over the web
    Conesa Mingo, P ; Gutierrez, J ; Quintana, A ; de la Rosa Trevin, JM ; Zaldivar-Peraza, A ; Cuenca Alba, J ; Kazemi, M ; Vargas, J ; del Cano, L ; Segura, J ; Sorzano, COS ; Maria Carazo, J (WILEY, 2018-01-01)
    Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here, we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to nonexpert users in need of very precise answers at several key stages of the structural elucidation process.
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    ENRICH: a fast method to improve the quality of flexible macromolecular reconstructions
    Kazemi, M ; Sorzano, COS ; Des Georges, A ; Carazo, JM ; Vargas, J (Cold Spring Harbor Laboratory, 2018)
    Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio, then, partially circumventing many issues that impact obtaining high quality reconstructions from small data sets. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, which we discuss in the manuscript.
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    Improving 3D reconstructions of macromolecular conformations
    Kazemi, M ; Sorzano, COS ; Des Georges, A ; Carazo, J-M ; Vargas, J (International Union of Crystallography (IUCr), 2018-07-20)