Osipov Evgenii M, Strelkov Sergei V
Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49, Box 822, 3000 Leuven, Belgium.
ACS Omega. 2025 May 16;10(21):21024-21029. doi: 10.1021/acsomega.4c07417. eCollection 2025 Jun 3.
In multiple areas of molecular biology research, series of closely related atomic structures of biomacromolecules are routinely generated. In particular, rational structure-based drug design heavily relies on the structural analysis of experimentally determined complexes between the target protein and multiple designed ligands (small molecules or biologicals). Here, we introduce DDtrek, a system for alignment, evaluation, and presentation of such structural data. This system is implemented as a plugin for the highly popular molecular graphics software PyMOL. A special feature of DDtrek is visualization of the aligned ligand structures together with the corresponding experimental density maps obtained through X-ray crystallography or cryoelectron microscopy, providing for the assessment of atomic model reliability and partial disorder. DDtrek is a lightweight and user-friendly system that can be utilized by whole research teams. DDtrek is freely available for Windows, MacOS, and Linux from https://github.com/BiocrystLab/DDtrek.
在分子生物学研究的多个领域，通常会生成一系列密切相关的生物大分子原子结构。特别是，基于结构的合理药物设计严重依赖于对目标蛋白与多种设计配体（小分子或生物制剂）之间实验确定的复合物进行结构分析。在此，我们介绍DDtrek，一种用于此类结构数据的比对、评估和展示的系统。该系统作为高度流行的分子图形软件PyMOL的插件实现。DDtrek的一个特殊功能是将比对后的配体结构与通过X射线晶体学或冷冻电子显微镜获得的相应实验密度图一起可视化，从而评估原子模型的可靠性和部分无序性。DDtrek是一个轻量级且用户友好的系统，可供整个研究团队使用。可从https://github.com/BiocrystLab/DDtrek免费获取适用于Windows、MacOS和Linux的DDtrek。
