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DENFERTversion 2: extension ofab initiostructural modelling of hydrated biomolecules to the case of small-angle neutron scattering data

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      Abstract

      Following the introduction of the programDENFERT[Koutsioubas & Pérez (2013).J. Appl. Cryst. 46, 1884–1888], which takes into account the hydration layer around solvated biological molecules duringab initiorestorations of low-resolution molecular envelopes from small-angle X-ray scattering data, the present work introduces the second version of the program, which provides the ability to treat neutron scattering data sets. By considering a fully interconnected and hydrated model during the entire minimization process, it has been possible to simplify the user input and reach more objective shape reconstructions. Additionally, a new method is implemented for the subtraction of the contribution of internal inhomogeneities of biomolecules to the measured scattering. Validation of the overall approach is performed by successfully recovering the shape of various protein molecules from experimental neutron and X-ray solution scattering data.

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      Determination of the regularization parameter in indirect-transform methods using perceptual criteria

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        Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

         D.I. Svergun (1999)
        A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to find a configuration that fits the data while minimizing the interfacial area. Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.
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          CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

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            Author and article information

            Journal
            JACGAR
            Journal of Applied Crystallography
            J Appl Crystallogr
            International Union of Crystallography (IUCr)
            1600-5767
            April 2016
            March 2016
            : 49
            : 2
            : 690-695
            10.1107/S1600576716003393
            © 2016

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