Topological Analysis Reveals Multiple Pathways in Molecular Dynamics.

IF 5.5 1区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Chemical Theory and Computation Pub Date : 2025-10-09 DOI:10.1021/acs.jctc.5c00819

Luca Donati, Surahit Chewle, Dominik St Pierre, Vijay Natarajan, Marcus Weber

引用次数: 0

Abstract

Molecular Dynamics simulations are indispensable tools for comprehending the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of high dimensional data. In this work, we present Molecular Kinetics via Topology (MoKiTo), a novel approach that combines the ISOKANN algorithm to determine the membership function of a molecular system with a topological analysis tool inspired by the Mapper algorithm. Our strategy efficiently identifies and characterizes distinct molecular pathways, enabling the detection and visualization of critical conformational transitions and rare events. This method offers deeper insights into molecular mechanisms, facilitating the design of targeted interventions in drug discovery and protein engineering.

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拓扑分析揭示分子动力学的多种途径。

分子动力学模拟是理解生物分子动态行为不可缺少的工具，但由于大量的高维数据，从这些模拟中提取有意义的分子途径仍然具有挑战性。在这项工作中，我们提出了通过拓扑的分子动力学（MoKiTo），这是一种结合ISOKANN算法来确定分子系统的隶属函数和受Mapper算法启发的拓扑分析工具的新方法。我们的策略有效地识别和表征了不同的分子途径，使关键构象转变和罕见事件的检测和可视化成为可能。这种方法提供了对分子机制的更深入的了解，促进了药物发现和蛋白质工程中靶向干预的设计。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Chemical Theory and Computation 化学-物理：原子、分子和化学物理

CiteScore

9.90

自引率

16.40%

发文量

568

审稿时长

1 months

期刊介绍： The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.