ArticleQuarterly reviews of biophysics2024
Graph theory approaches for molecular dynamics simulations.
Article in Quarterly reviews of biophysics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Mapping Allosteric Communication in the Nucleosome with Conditional Activity.Journal of chemical information and modeling · 2026Article
- Mechanism of Hsp70 activation: How J-domain proteins push for ATP hydrolysis.PLoS computational biology · 2026Article
- Enhancing bioinformatics engineering by utilizing graph therapeutic properties for clinically approved antitoxin drugs in zoonotic diseases.Scientific reports · 2026Article
- Computation and deep-learning-driven advances in CRISPR genome editing.Nature structural & molecular biology · 2026Review
- Mutation and ACE2-induced allosteric network rewiring in Delta and Omicron SARS-CoV-2 spike proteins.Biophysical journal · 2026Article
- Inferences on the Watts-Strogatz Model: A Study on Brain Functional Connectivity.Neuroinformatics · 2025Article
- Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins.bioRxiv : the preprint server for biology · 2025Article
- Clustering and Analyzing Ensembles of Residue Interaction Networks from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Article
- Molecular Mechanisms of Silicone Network Formation: Bridging Scales from Curing Reactions to Percolation and Entanglement Analyses.Polymers · 2025Article
- Mapping Allosteric Communication in the Nucleosome with Conditional Activity.bioRxiv : the preprint server for biology · 2025Article
- Design Rules for Expanding PAM Compatibility in CRISPR-Cas9 from the VQR, VRER and EQR variants.bioRxiv : the preprint server for biology · 2025Article
- MDGraphEmb: a toolkit for graph embedding and classification of protein conformational ensembles.Bioinformatics (Oxford, England) · 2025Article
- Graph Attention Neural Networks Reveal TnsC Filament Assembly in a CRISPR-Associated Transposon.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.