Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Acta Crystallogr D Struct Biol. 2021 Jun 1;77(Pt 6):712-726. doi: 10.1107/S2059798321001753. Epub 2021 May 19.
In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application of link-annotation records to structural models to ensure the correct treatment of individual instances of covalent linkages. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. A number of tools to facilitate the practical modelling of covalent linkages available within the CCP4 suite are described, including a new restraint-dictionary accumulator, the Make Covalent Link tool and AceDRG interface in Coot, the 3D graphical editor JLigand and the mechanisms for dealing with covalent linkages in the CCP4i2 and CCP4 Cloud environments. These integrated solutions streamline and ease the covalent-linkage modelling workflow, seamlessly transferring relevant information between programs. Current recommended practice is elucidated by means of instructive practical examples. By summarizing the different approaches to modelling linkages that are available within the CCP4 suite, limitations and potential pitfalls that may be encountered are highlighted in order to raise awareness, with the intention of improving the quality of future modelled covalent linkages in macromolecular complexes.
在本贡献中，考虑了当前在 CCP4 套件中建模共价键的协议。回顾了用于建模共价键的机制：使用字典来描述由于共价键而导致的立体化学变化，以及应用链接注释记录到结构模型中，以确保正确处理共价键的各个实例。以前，与当代组件字典相比，链接描述的质量较差。因此，已经对 AceDRG 进行了改编，以生成与单个组件质量相同的链接字典。概述了 AceDRG 用于生成链接字典的方法，包括对链接组件的相关修改。描述了 CCP4 套件中可用的一些方便实用的共价键建模工具，包括新的约束字典累加器、Make Covalent Link 工具和 Coot 中的 AceDRG 接口、3D 图形编辑器 JLigand 以及 CCP4i2 和 CCP4 Cloud 环境中处理共价键的机制。这些集成解决方案简化并简化了共价键建模工作流程，在程序之间无缝传输相关信息。通过示例说明当前的推荐实践。通过总结 CCP4 套件中可用的不同建模链接方法，突出了可能遇到的限制和潜在陷阱，以提高认识，旨在提高未来大分子复合物中建模共价键的质量。
