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- W4319937598 abstract "Molecular interactions are key to regulating cellular processes by transferring information between distant sites, promoting protein complex formation or enzyme activation. Understanding how biomolecules orchestrate this information transfer is critical to gaining insight into biochemical processes, modulating them through bioengineering, or even controlling reactions through small-molecule activators. In the past decade, network theory has been applied to identify molecular features and allosteric hubs essential for establishing information transfer in biomolecules. Molecular dynamics simulations often are the source of time-correlated data that is used to construct protein networks, which can be rationalized in terms of different correlation metrics. The specific molecular features and correlation metrics to use for reliably describing the coupled motions underlying allostery are often overlooked concepts. In this work, we provide a Python software package for performing network analysis on the molecular dynamics of biological systems. MDigest has a modular structure that allows for rapid evaluation and straightforward comparison of residue couplings obtained from different molecular features and various correlation metrics. In addition to commonly used features such as generalized correlation based on atomic displacements or covariance of dihedral angle fluctuations, we include a new network approach that relies on the correlation of electrostatic couplings over time, resulting in a coordinate-independent and physically relevant representation of the allosteric network. Besides allowing for efficient comparison of different networks at custom distance thresholding, our implementation allows the user to compare and contrast the underlying community structures and determine optimal paths for the most informative graph. Our enhanced and extended protocol allows for rigorous and comprehensive analysis of MD trajectories from small to large macromolecular complexes." @default.
- W4319937598 created "2023-02-11" @default.
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- W4319937598 date "2023-02-01" @default.
- W4319937598 modified "2023-09-25" @default.
- W4319937598 title "MDigest: A comprehensive toolkit for detection of allosteric communication from molecular dynamics simulations of biochemical systems" @default.
- W4319937598 doi "https://doi.org/10.1016/j.bpj.2022.11.469" @default.
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