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- Agirre, Jon, et al.
(författare)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Tidskriftsartikel (refereegranskat)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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| 2. |
- Berruyer, P., et al.
(författare)
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Imaging Radial Distribution Functions of Complex Particles by Relayed Dynamic Nuclear Polarization
- 2023
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Ingår i: Journal of the American Chemical Society. - 0002-7863. ; 145:17, s. 9700-9707
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Tidskriftsartikel (refereegranskat)abstract
- The physical properties of many modern multi-component materials are determined by their internal microstructure. Tools capable of characterizing complex nanoscale architectures in composite materials are, therefore, essential to design materials with targeted properties. Depending on the morphology and the composition, structures may be measured by laser diffraction, scattering methods, or by electron microscopy. However, it can be difficult to obtain contrast in materials where all the components are organic, which is typically the case for formulated pharmaceuticals, or multi-domain polymers. In nuclear magnetic resonance (NMR) spectroscopy, chemical shifts allow a clear distinction between organic components and can in principle provide the required chemical contrast. Here, we introduce a method to obtain radial images of the internal structure of multi-component particles from NMR measurements of the relay of nuclear hyperpolarization obtained from dynamic nuclear polarization. The method is demonstrated on two samples of hybrid core-shell particles composed of a core of polystyrene with a shell of mesostructured silica filled with the templating agent CTAB and is shown to yield accurate images of the core-shell structures with a nanometer resolution.
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| 4. |
- Cordova, M., et al.
(författare)
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Atomic-level structure determination of amorphous molecular solids by NMR
- 2023
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Ingår i: Nature Communications. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder leads to a high degree of overlap between measured signals, and prevents the unambiguous identification of a single modeled periodic structure as representative of the whole material. Here, we determine the atomic-level ensemble structure of the amorphous form of the drug AZD4625 by combining solid-state NMR experiments with molecular dynamics (MD) simulations and machine-learned chemical shifts. By considering the combined shifts of all 1H and 13C atomic sites in the molecule, we determine the structure of the amorphous form by identifying an ensemble of local molecular environments that are in agreement with experiment. We then extract and analyze preferred conformations and intermolecular interactions in the amorphous sample in terms of the stabilization of the amorphous form of the drug.
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| 9. |
- Read, Randy J., et al.
(författare)
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A New Generation of Crystallographic Validation Tools for the Protein Data Bank
- 2011
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 19:10, s. 1395-1412
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Tidskriftsartikel (refereegranskat)abstract
- This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a now assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.
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| 10. |
- Richards, David A, et al.
(författare)
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Integrating quantitative and qualitative data and findings when undertaking randomised controlled trials.
- 2019
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Ingår i: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 9:11
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Tidskriftsartikel (refereegranskat)abstract
- It is common to undertake qualitative research alongside randomised controlled trials (RCTs) when evaluating complex interventions. Researchers tend to analyse these datasets one by one and then consider their findings separately within the discussion section of the final report, rarely integrating quantitative and qualitative data or findings, and missing opportunities to combine data in order to add rigour, enabling thorough and more complete analysis, provide credibility to results, and generate further important insights about the intervention under evaluation. This paper reports on a 2 day expert meeting funded by the United Kingdom Medical Research Council Hubs for Trials Methodology Research with the aims to identify current strengths and weaknesses in the integration of quantitative and qualitative methods in clinical trials, establish the next steps required to provide the trials community with guidance on the integration of mixed methods in RCTs and set-up a network of individuals, groups and organisations willing to collaborate on related methodological activity. We summarise integration techniques and go beyond previous publications by highlighting the potential value of integration using three examples that are specific to RCTs. We suggest that applying mixed methods integration techniques to data or findings from studies involving both RCTs and qualitative research can yield insights that might be useful for understanding variation in outcomes, the mechanism by which interventions have an impact, and identifying ways of tailoring therapy to patient preference and type. Given a general lack of examples and knowledge of these techniques, researchers and funders will need future guidance on how to undertake and appraise them.
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