Topological analysis reveals multiple pathways in molecular dynamics

TL;DR

This paper introduces MoKiTo, a novel topological approach combining ISOKANN and Mapper algorithms to identify and analyze multiple molecular pathways from molecular dynamics simulations, enhancing understanding of biomolecular conformational changes.

Contribution

The paper presents a new method that integrates topology and reaction coordinate analysis to better detect and visualize molecular pathways in MD simulations.

Findings

Efficient identification of multiple molecular pathways.

Enhanced visualization of conformational transitions.

Deeper insights into biomolecular mechanisms.

Abstract

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.