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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >Conformation-independent structural comparison of macromolecules with ProSMART
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Conformation-independent structural comparison of macromolecules with ProSMART

机译：Conformation-independent结构的比较大分子与绰越

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摘要

The identification and exploration of (dis) similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing pool of structural data into a more readily accessible form, potentially offering biological insight or influencing subsequent experiments.
机译：识别和探索(dis)大分子结构的相似性可以帮助获得生物见解,例如当可视化或量化的反应蛋白质配体绑定。通常是一个一致性比较结构这样的比较分析的先决条件。蛋白质的构象变化戏剧性的,传统的校准方法努力提供一个直观的解决方案简单的分析。普罗克汝斯忒斯更容易,结构性的匹配校准和限制工具(绰越)开发,实现了吗conformation-independent结构对齐等提供额外的功能作为一代使用的限制大分子模型的细化。比较蛋白质或DNA / RNA结构构象变化的存在通过执行链和域刚性。通过流行molecular-graphics软件如CCP4mg和PyMOL提供直观的反馈关于结构保护和微妙的差异关闭同系物,否则很难识别。对应于各种residue-based分数提供的信息,从而使评估的保护的骨干和侧链构象相对于当地的坐标框架。绰越能帮助打破复杂性伴随着不断的增长结构数据更容易访问形式,可能提供生物见解或影响后续的实验。

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