The Experts below are selected from a list of 218313 Experts worldwide ranked by ideXlab platform
Kenneth Shankland - One of the best experts on this subject based on the ideXlab platform.
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Structure Determination from Powder Diffraction Data - Structure Determination from powder diffraction data.
Acta Crystallographica Section A Foundations of Crystallography, 2007Co-Authors: William I. F. David, Kenneth ShanklandAbstract:Advances made over the past decade in Structure Determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal Structures, new methods are required to make the solution of inorganic crystal Structures more routine. The use of complementary techniques such as NMR to assist Structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for Structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of Structure Determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal Structures over the next decade are assessed.
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Structure Determination from powder diffraction data.
Acta crystallographica. Section A Foundations of crystallography, 2007Co-Authors: William I. F. David, Kenneth ShanklandAbstract:Advances made over the past decade in Structure Determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal Structures, new methods are required to make the solution of inorganic crystal Structures more routine. The use of complementary techniques such as NMR to assist Structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for Structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of Structure Determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal Structures over the next decade are assessed.
William I. F. David - One of the best experts on this subject based on the ideXlab platform.
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Structure Determination from Powder Diffraction Data - Structure Determination from powder diffraction data.
Acta Crystallographica Section A Foundations of Crystallography, 2007Co-Authors: William I. F. David, Kenneth ShanklandAbstract:Advances made over the past decade in Structure Determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal Structures, new methods are required to make the solution of inorganic crystal Structures more routine. The use of complementary techniques such as NMR to assist Structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for Structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of Structure Determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal Structures over the next decade are assessed.
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Structure Determination from powder diffraction data.
Acta crystallographica. Section A Foundations of crystallography, 2007Co-Authors: William I. F. David, Kenneth ShanklandAbstract:Advances made over the past decade in Structure Determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal Structures, new methods are required to make the solution of inorganic crystal Structures more routine. The use of complementary techniques such as NMR to assist Structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for Structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of Structure Determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal Structures over the next decade are assessed.
Paul D. Adams - One of the best experts on this subject based on the ideXlab platform.
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Macromolecular X-ray Structure Determination using weak, single-wavelength anomalous data
Nature Methods, 2015Co-Authors: Gábor Bunkóczi, Paul D. Adams, Ralf W. Grosse-kunstleve, Airlie J Mccoy, Nathaniel Echols, James M Holton, Randy J Read, Thomas C TerwilligerAbstract:We describe a likelihood-based method for determining the subStructure of anomalously scattering atoms in macromolecular crystals that allows successful Structure Determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases. An improved analysis approach for single-wavelength anomalous diffraction (SAD)-based macromolecular X-ray Structure Determination expands the applicability of this phasing method for macromolecules with weak anomalous signals.
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Recent developments in software for the automation of crystallographic macromolecular Structure Determination.
Current opinion in structural biology, 2000Co-Authors: Paul D. Adams, Ralf W. Grosse-kunstleveAbstract:The automation of macromolecular Structure Determination by X-ray crystallography has long been a goal for many researchers. Recently, there have been improvements in the underlying algorithms, some of which have been implemented in software packages that deal with multiple stages of the Structure Determination process. These first steps towards complete automation have made X-ray crystallography more efficient.
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Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Acta Crystallographica Section D Biological Crystallography, 1998Co-Authors: Axel T. Brunger, Paul D. Adams, G. M. Clore, W. L. Delano, Piet Gros, R.w. Grosse-kunstleve, Jiansheng Jiang, J. Kuszewski, Navraj S. PannuAbstract:A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular Structure Determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing Structure-Determination programs the architecture of CNS is highly flexible, allowing for extension to other Structure-Determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical Structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic Structure-Determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data Structures, such as Structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular Structure Determination by X-ray crystallography and solution NMR.
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crystallography nmr system a new software suite for macromolecular Structure Determination
Acta Crystallographica Section D-biological Crystallography, 1998Co-Authors: Axel T. Brunger, Paul D. Adams, G. M. Clore, W. L. Delano, Piet Gros, Jiansheng Jiang, R W Grossekunstleve, J. KuszewskiAbstract:A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular Structure Determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing Structure-Determination programs the architecture of CNS is highly flexible, allowing for extension to other Structure-Determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical Structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic Structure-Determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data Structures, such as Structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular Structure Determination by X-ray crystallography and solution NMR.
Maryjane Tremayne - One of the best experts on this subject based on the ideXlab platform.
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contemporary advances in the use of powder x ray diffraction for Structure Determination
Angewandte Chemie, 2001Co-Authors: Kenneth D. M. Harris, Maryjane Tremayne, Benson M KariukiAbstract:Many crystalline solids cannot be prepared in the form of single crystals of sufficient size and/or quality for investigation using single-crystal X-ray diffraction techniques, and the opportunity to carry out Structure Determination using powder diffraction data is therefore essential to understand the structural properties of such materials. Although the refinement stage of the Structure Determination process can be carried out fairly routinely from powder diffraction data using the Rietveld profile refinement technique, solving crystal Structures directly from powder data is associated with several intrinsic difficulties. Nevertheless, substantial progress has been made in recent years in the scope and potential of techniques in this field. This article aims to highlight the types of structural problems for which Structure Determination may now be tackled directly from powder diffraction data, and contemporary applications across several chemical disciplines are presented. A brief survey of the underlying methodologies is given, with some emphasis on recently developed techniques for carrying out the Structure-solution stage of the Structure-Determination process.
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Crystal Structure Determination from Powder Diffraction Data
Chemistry of Materials, 1996Co-Authors: Kenneth D. M. Harris, Maryjane TremayneAbstract:A wide range of important crystalline solids cannot be prepared in the form of single crystals of suitable size and quality for structural characterization by conventional single-crystal X-ray diffraction methods. The development of techniques for crystal Structure Determination from powder diffraction data is clearly important for allowing the structural characterization of such materials. Although the Structure refinement stage of the Structure Determination process can now be carried out fairly routinely using the Rietveld profile refinement technique, Structure solution directly from powder diffraction data is associated with several intrinsic difficulties. The article surveys the field of crystal Structure Determination from powder diffraction data. Particular emphasis is given to the challenging Structure solution stage of the Structure Determination process, with illustrative case studies highlighting the features of each of the main methods that are currently used for Structure solution from powde...
Sjors H W Scheres - One of the best experts on this subject based on the ideXlab platform.
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Amyloid Structure Determination in RELION-3.1.
Acta crystallographica. Section D Structural biology, 2020Co-Authors: Sjors H W ScheresAbstract:Helical reconstruction in RELION is increasingly being used to determine the atomic Structures of amyloid filaments from electron cryo-microscopy (cryo-EM) images. However, because the energy landscape of amyloid refinements is typically fraught with local optima, amyloid Structure Determination is often difficult. This paper aims to help RELION users in this process. It discusses aspects of helical reconstruction that are particularly relevant to amyloids, it illustrates the problem of local optima in refinement and how to detect them, and it introduces a new method to calculate 3D initial models from reference-free 2D class averages. By providing starting models that are closer to the global optimum, this method makes amyloid Structure Determination easier. All methods described are open-source and distributed within RELION-3.1. Their use is illustrated using a publicly available data set on tau filaments from the brain of an individual with Alzheimer's disease.
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Amyloid Structure Determination in RELION-3.1
2019Co-Authors: Sjors H W ScheresAbstract:Helical reconstruction in RELION is increasingly used to determine atomic Structures of amyloid filaments from electron cryo-microscopy (cryo-EM) images. However, because the energy landscape of amyloid refinements is typically fraught with local optima, amyloid Structure Determination is often difficult. This paper aims to help RELION users in this process. It discusses aspects of helical reconstruction that are specific to amyloids; it illustrates the problem of local optima in refinement and how to detect these; and it introduces a new method to calculate 3D initial models from reference-free 2D class averages. By providing starting models that are closer to the global optimum, this method makes amyloid Structure Determination easier. All methods described are open-source and distributed within RELION-3.1. Their use is illustrated using a publicly available data set on tau filaments from the brain of an individual with Alzheimer’s disease.
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accelerated cryo em Structure Determination with parallelisation using gpus in relion 2
eLife, 2016Co-Authors: Dari Kimanius, Sjors H W Scheres, Bjorn O Forsberg, Erik LindahlAbstract:By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM Structure Determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM Structure Determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM Structure Determination in a matter of days on a single workstation.
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A Bayesian view on cryo-EM Structure Determination
2012 9th IEEE International Symposium on Biomedical Imaging (ISBI), 2012Co-Authors: Sjors H W ScheresAbstract:Three-dimensional (3D) Structure Determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires many parameters to be determined from extremely noisy data. This makes the method prone to overfitting, that is, when Structures describe noise rather than signal, in particular near their resolution limit where noise levels are highest. Cryo-EM Structures are typically filtered using ad hoc procedures to prevent overfitting, but the tuning of arbitrary parameters may lead to subjectivity in the results. I describe a Bayesian interpretation of cryo-EM Structure Determination, where smoothness in the reconstructed density is imposed through a Gaussian prior in the Fourier domain. The statistical framework dictates how data and prior knowledge should be combined, so that the optimal 3D linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained. Application to experimental data indicates that the statistical approach yields more reliable Structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different Structures.
