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首页> 外文期刊>Acta crystallographica. Section D, Structural biology. >Improved ligand geometries in crystallographic refinement using AFITT AFITT in PHENIX PHENIX
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Improved ligand geometries in crystallographic refinement using AFITT AFITT in PHENIX PHENIX

机译：提高配体晶体的几何图形改进使用AFITT AFITT在凤凰凤凰

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摘要

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data‐to‐parameter ratio. While the classical Engh and Huber restraints work well for standard amino‐acid residues, the chemical complexity of small‐molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX – AFITT refinement uses a full molecular‐mechanics force field for user‐selected small‐molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high‐quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high‐throughput workflows. PHENIX – AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein–ligand PDB structures are presented. Refinements using PHENIX – AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX – AFITT refinements result in more chemically accurate models for small‐molecule ligands.
机译：现代晶体结构细化项目的依赖在几何约束克服挑战一个低数据量参数的比例。古典恩格和Huber限制适用标准氨基酸高酸残留的化学复杂的小分子配体提供了一个特别的挑战。配位体约束限制那些可以很容易描述的晶体信息文件(CIF)格式,从而牺牲化学的灵活性和充满活力的准确性,或他们雇佣协议大大延长细化时间,可能阻碍快速自动细化工作流程。改进使用一个完整的分子力学的力量领域为用户提供有关选择小分子配体在改进,消除潜在的找到或生成的难题高质量的几何约束。与标准的细化协议集成并要求几乎没有额外的步骤用户,使其适合高吞吐量工作流。多个配体在一个模型中,备用构象和共价结合配体。结合AFITT和凤凰的结果189年软件套件的数据集protein-ligand PDB结构。使用凤凰——AFITT显著细化能源和导致减少配体构象改进的几何图形不损害健康实验数据。凤凰——AFITT细化导致更多化学精确模型为小分子配体。

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