Structures of membrane proteins are challenging to determine experimentally and currently represent only about 2% of the structures in the ProteinDataBank. Because of this disparity, methods for modeling membrane proteins are fewer and of lower quality than those for modeling soluble proteins. However, better expression, crystallization, and cryo-EM techniques have prompted a recent increase in experimental structures of membrane proteins, which can act as templates to predict the structure of closely related proteins through homology modeling. Because homology modeling relies on a structural template, it is easier and more accurate than fold recognition methods or de novo modeling, which are used when the sequence similarity between the query sequence and the sequence of related proteins in structural databases is below 25%. In homology modeling, a query sequence is mapped onto the coordinates of a single template and refined. With the increase in available templates, several templates often cover overlapping segments of the query sequence. Multi-template modeling can be used to identify the best template for local segments and join them into a single model. Here we provide a protocol for modeling membrane proteins from multiple templates in the Rosetta software suite. This approach takes advantage of several integrated frameworks, namely RosettaScripts, RosettaCM, and RosettaMP with the membrane scoring function.

中文翻译：

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使用多模板同源性建模对膜蛋白进行建模的特异性

膜蛋白的结构很难通过实验确定，目前仅占ProteinDataBank结构的约2％。由于这种差异，用于建模膜蛋白的方法比用于建模可溶性蛋白的方法少且质量低。然而，更好的表达，结晶和cryo-EM技术促进了膜蛋白实验结构的最新发展，该膜蛋白可以作为模板，通过同源性建模预测紧密相关的蛋白的结构。因为同源性建模依赖于结构模板，所以它比折叠识别方法或从头建模更容易，更准确，当在结构数据库中查询序列和相关蛋白序列之间的序列相似性低于25％时，可以使用这种方法。在同源性建模中 将查询序列映射到单个模板的坐标上并进行优化。随着可用模板的增加，几个模板通常覆盖查询序列的重叠部分。多模板建模可用于为局部细分确定最佳模板，并将它们加入单个模型中。在这里，我们提供了一种在Rosetta软件套件中从多个模板对膜蛋白进行建模的协议。这种方法利用了具有膜评分功能的多个集成框架，即RosettaScripts，RosettaCM和RosettaMP。多模板建模可用于为局部细分确定最佳模板，并将它们加入单个模型中。在这里，我们提供了一种在Rosetta软件套件中从多个模板对膜蛋白进行建模的协议。这种方法利用了具有膜评分功能的多个集成框架，即RosettaScripts，RosettaCM和RosettaMP。多模板建模可用于为局部细分确定最佳模板，并将它们加入单个模型中。在这里，我们提供了一种在Rosetta软件套件中从多个模板对膜蛋白进行建模的协议。这种方法利用了具有膜评分功能的多个集成框架，即RosettaScripts，RosettaCM和RosettaMP。