Patel Amun C, Sinha Souvik, Palermo Giulia
Department of Bioengineering, University of California Riverside, 900 University Avenue, 92521, Riverside, CA, United States.
Department of Chemistry, University of California Riverside, 900 University Avenue, 92521, Riverside, CA52512, United States.
Q Rev Biophys. 2024 Dec 10;57:e15. doi: 10.1017/S0033583524000143.
Graph theory, a branch of mathematics that focuses on the study of graphs (networks of nodes and edges), provides a robust framework for analysing the structural and functional properties of biomolecules. By leveraging molecular dynamics (MD) simulations, atoms or groups of atoms can be represented as nodes, while their dynamic interactions are depicted as edges. This network-based approach facilitates the characterization of properties such as connectivity, centrality, and modularity, which are essential for understanding the behaviour of molecular systems. This review details the application and development of graph theory-based models in studying biomolecular systems. We introduce key concepts in graph theory and demonstrate their practical applications, illustrating how innovative graph theory approaches can be employed to design biomolecular systems with enhanced functionality. Specifically, we explore the integration of graph theoretical methods with MD simulations to gain deeper insights into complex biological phenomena, such as allosteric regulation, conformational dynamics, and catalytic functions. Ultimately, graph theory has proven to be a powerful tool in the field of molecular dynamics, offering valuable insights into the structural properties, dynamics, and interactions of molecular systems. This review establishes a foundation for using graph theory in molecular design and engineering, highlighting its potential to transform the field and drive advancements in the understanding and manipulation of biomolecular systems.
图论是数学的一个分支，专注于研究图（节点和边的网络），为分析生物分子的结构和功能特性提供了一个强大的框架。通过利用分子动力学（MD）模拟，原子或原子组可以表示为节点，而它们的动态相互作用则描绘为边。这种基于网络的方法有助于表征诸如连通性、中心性和模块化等特性，这些特性对于理解分子系统的行为至关重要。本文详细介绍了基于图论的模型在研究生物分子系统中的应用和发展。我们介绍了图论中的关键概念，并展示了它们的实际应用，说明了如何采用创新的图论方法来设计具有增强功能的生物分子系统。具体而言，我们探讨了图论方法与MD模拟的整合，以更深入地了解复杂的生物现象，如变构调节、构象动力学和催化功能。最终，图论已被证明是分子动力学领域的一个强大工具，为分子系统的结构特性、动力学和相互作用提供了有价值的见解。本文为在分子设计和工程中使用图论奠定了基础，突出了其改变该领域以及推动生物分子系统理解和操纵方面进展的潜力。
