Topological analysis reveals multiple pathways in molecular dynamics
Fuente:
arXiv
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| Autori principali: | , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| Soggetti: | |
| Accesso online: | |
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| _version_ | 1866929659440005120 |
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| author | Donati, Luca Chewle, Surahit Pierre, Dominik St. Natarajan, Vijay Weber, Marcus |
| author_facet | Donati, Luca Chewle, Surahit Pierre, Dominik St. Natarajan, Vijay Weber, Marcus |
| contents | Molecular Dynamics simulations are essential tools for understanding the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of generated data. In this work, we present Molecular Kinetics via Topology (MoKiTo), a novel approach that combines the ISOKANN algorithm to determine the reaction coordinate of a molecular system with a topological analysis 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2412_20580 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Topological analysis reveals multiple pathways in molecular dynamics Donati, Luca Chewle, Surahit Pierre, Dominik St. Natarajan, Vijay Weber, Marcus Chemical Physics Molecular Dynamics simulations are essential tools for understanding the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of generated data. In this work, we present Molecular Kinetics via Topology (MoKiTo), a novel approach that combines the ISOKANN algorithm to determine the reaction coordinate of a molecular system with a topological analysis 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. |
| title | Topological analysis reveals multiple pathways in molecular dynamics |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2412.20580 |