Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina 188300, Russia.
Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia.
J Chem Inf Model. 2024 Aug 26;64(16):6241-6246. doi: 10.1021/acs.jcim.3c02087. Epub 2024 Aug 9.
This work introduces a new faster implementation of the hydrogen bond network (complex arrangement of hydrogen bonds between or within molecules) search algorithm in biomacromolecules and their environment. Existing implementation of such an algorithm in GROMACS [Abraham et al. . 2024.] has limitations in the analysis of large structures and trajectories. The new implementation, in the form of a native GROMACS trajectory analysis module, allows for quick analysis of molecular dynamics trajectories without restrictions, thus overcoming the limitations of the original algorithm. The application of the developed method enabled the acquisition and analysis of hydrogen bond networks in the studied defensin-like protein , as well as the study of hydrogen bond occupancies between the protein's residues and water molecules. The data obtained using the new implementation coincided with the experimental data.
这项工作介绍了一种新的更快的生物大分子及其环境中氢键网络（分子间或分子内氢键的复杂排列）搜索算法的实现方法。GROMACS [Abraham 等人，2024] 中现有此类算法的实现方法在分析大型结构和轨迹方面存在限制。新的实现形式是一个本地 GROMACS 轨迹分析模块，允许快速无限制地分析分子动力学轨迹，从而克服了原始算法的限制。所开发方法的应用使得能够在研究的防御素样蛋白中获取和分析氢键网络，并研究蛋白质残基与水分子之间的氢键占有率。使用新实现方法获得的数据与实验数据一致。
