This protocol describes a workflow for creating structural models of proteins or protein complexes using distance restraints derived from cross-linking mass spectrometry experiments. The distance restraints are used (i) to adjust preliminary models that are calculated on the basis of a homologous template and primary sequence, and (ii) to select the model that is in best agreement with the experimental data. In the case of protein complexes, the cross-linking data are further used to dock the subunits to one another to generate models of the interacting proteins. Predicting models in such a manner has the potential to indicate multiple conformations and dynamic changes that occur in solution. This modeling protocol is compatible with many cross-linking workflows and uses open-source programs or programs that are free for academic users and do not require expertise in computational modeling. This protocol is an excellent additional application with which to use cross-linking results for building structural models of proteins. The established protocol is expected to take 6-12 d to complete, depending on the size of the proteins and the complexity of the cross-linking data.

中文翻译：

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使用源自交联质谱数据的距离约束对蛋白质模型进行结构预测。

该协议描述了使用源自交联质谱实验的距离约束创建蛋白质或蛋白质复合物的结构模型的工作流程。距离约束用于 (i) 调整基于同源模板和一级序列计算的初步模型，以及 (ii) 选择与实验数据最一致的模型。在蛋白质复合物的情况下，交联数据进一步用于将亚基相互对接以生成相互作用蛋白质的模型。以这种方式预测模型有可能表明溶液中发生的多种构象和动态变化。该建模协议与许多交叉链接工作流兼容，并使用开源程序或对学术用户免费且不需要计算建模专业知识的程序。该协议是一个出色的附加应用程序，可用于使用交联结果构建蛋白质结构模型。已建立的协议预计需要 6-12 天才能完成，具体取决于蛋白质的大小和交联数据的复杂性。