Optimod - An automated approach for constructing and optimizing initial models for single-particle electron microscopy
Optimod - An automated approach for constructing and optimizing initial models for single-particle electron microscopy
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DOI：
10.1016/j.jsb.2013.10.009
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发表时间：
2013-12-01
影响因子：
3
通讯作者：
Carragher, Bridget
中科院分区：
文献类型：
--
作者：
Lyumkis, Dmitry;Vinterbo, Staal;Carragher, Bridget
单粒子冷冻电子显微镜现在已被良好确定为大型大分子和大分子复合物结构表征的技术。原始数据非常嘈杂，由二维预测组成，必须从中重建3D生物学对象。 3D对象取决于对分配给2D投影图像的正确角度方向的知识。已经开发了许多算法来确定2D图像之间的相对角度取向，但是从2D到3D的过渡仍然具有挑战性，并且可能导致错误和冲突的结果。在这里，我们描述了一个通用的，自动化的过程，称为OptimOD，用于使用公共线方法重建和优化3D模型。 OptimOD近似于方向角，并从2D类平均重建独立的地图。然后，它迭代过程，同时将每个地图视为需要将其与其他可能结果进行比较的原始解决方案。我们合并了3D对齐，聚类和改进的过程，以优化每个地图以及标准评分指标，以促进最佳模型的选择。我们还表明，可以将小角度倾斜对数据作为评分指标之一，以改善最佳初始模型的选择，并提供验证检查。使用两个实验性冷冻EM数据集证明了总体方法 - 80年代的核糖体代表了从头开始重建的相对简单的情况，而TF-TFR复合物则代表了一个具有挑战性的情况，以前已证明它可以同样提供多个同样的案例。最初模型问题的合理解决方案。 （c）2013 Elsevier Inc.保留所有权利。
Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets - the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem. (C) 2013 Elsevier Inc. All rights reserved.