ArticleBioinformatics and biology insights2008
Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives.
Article in Bioinformatics and biology insights, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Predicting protein-nucleic acid flexibility using persistent sheaf Laplacians.Physical chemistry chemical physics : PCCP · 2026Article
- Persistent Sheaf Laplacian Analysis of Protein Flexibility.The journal of physical chemistry. B · 2025Article
- Multiscale Differential Geometry Learning for Protein Flexibility Analysis.Journal of computational chemistry · 2025Article
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- Protein Dynamics to Define and Refine Disordered Protein Ensembles.The journal of physical chemistry. B · 2022Article
- Unraveling the Compositional and Molecular Features Involved in Lysozyme-Benzothiazole Derivative Interactions.Molecules (Basel, Switzerland) · 2021Article
- "Dividing and Conquering" and "Caching" in Molecular Modeling.International journal of molecular sciences · 2021Review
- Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis.Journal of applied and computational topology · 2020Article
- A review of mathematical representations of biomolecular data.Physical chemistry chemical physics : PCCP · 2020Review
- MathDL: mathematical deep learning for D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- When Stiffness Matters: Mechanosensing in Heart Development and Disease.Frontiers in cell and developmental biology · 2020Review
- AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening.Journal of chemical information and modeling · 2019Article
- Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.Journal of computational chemistry · 2016Article
- Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM).The Journal of chemical physics · 2015Article
- Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.PLoS computational biology · 2015Article
- Multidimensional persistence in biomolecular data.Journal of computational chemistry · 2015Article
- Persistent homology analysis of protein structure, flexibility, and folding.International journal for numerical methods in biomedical engineering · 2014Article
- Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis.The Journal of chemical physics · 2014Article
- Molecular nonlinear dynamics and protein thermal uncertainty quantification.Chaos (Woodbury, N.Y.) · 2014Article
- Multiscale multiphysics and multidomain models--flexibility and rigidity.The Journal of chemical physics · 2013Article
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Authors and funding
2 authors.
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Abstract
In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of 'open to close' (open-->close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series.
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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.