Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
Acta Crystallogr D Struct Biol. 2022 Sep 1;78(Pt 9):1090-1098. doi: 10.1107/S2059798322007732. Epub 2022 Aug 25.
Interactive model building can be a difficult and time-consuming step in the structure-solution process. Automated model-building programs such as Buccaneer often make it quicker and easier by completing most of the model in advance. However, they may fail to do so with low-resolution data or a poor initial model or map. The Buccaneer pipeline is a relatively simple program that iterates Buccaneer with REFMAC to refine the model and update the map. A new pipeline called ModelCraft has been developed that expands on this to include shift-field refinement, machine-learned pruning of incorrect residues, classical density modification, addition of water and dummy atoms, building of nucleic acids and final rebuilding of side chains. Testing was performed on 1180 structures solved by experimental phasing, 1338 structures solved by molecular replacement using homologues and 2030 structures solved by molecular replacement using predicted AlphaFold models. Compared with the previous Buccaneer pipeline, ModelCraft increased the mean completeness of the protein models in the experimental phasing cases from 91% to 95%, the molecular-replacement cases from 50% to 78% and the AlphaFold cases from 82% to 91%.
交互式建模在结构解析过程中可能是困难且耗时的步骤。自动建模程序（如 Buccaneer）通常可以通过预先完成大部分模型来更快、更轻松地完成建模。然而，在低分辨率数据或初始模型或地图较差的情况下，它们可能无法完成建模。Buccaneer 管道是一个相对简单的程序，它使用 REFMAC 迭代 Buccaneer 以精修模型并更新地图。已经开发了一个名为 ModelCraft 的新管道，该管道在此基础上进行了扩展，包括移位场精修、基于机器学习的不正确残基修剪、经典密度修正、水和虚拟原子的添加、核酸的构建以及侧链的最终重建。在 1180 个通过实验相位解析解决的结构、1338 个使用同源物进行分子替换解决的结构和 2030 个使用预测的 AlphaFold 模型进行分子替换解决的结构上进行了测试。与以前的 Buccaneer 管道相比，ModelCraft 将实验相位解析案例中蛋白质模型的平均完整性从 91%提高到 95%，分子替换案例从 50%提高到 78%，AlphaFold 案例从 82%提高到 91%。
