ReviewInternational journal of molecular sciences2018
Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.
Review in International journal of molecular sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed.
- Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.Proteins · 2026Article
- Characterization of Membrane Binding and Protein-Lipid Interactions at the Atomic Level with an Accelerated HMMM Model.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Optimizing a coarse-grained model for large-scale membrane protein simulation.Biophysical reports · 2025Article
- Differential conformational expansion of NUP98-HOXA9 oncoprotein from nanosized assemblies to macrophases.Nature communications · 2025Article
- Martini 3 coarse-grained model of enzymes: Framework with validation by all-atom simulations and x-ray diffraction measurements.The Journal of chemical physics · 2025Article
- Explainable machine learning for predicting distant metastases in renal cell carcinoma patients: a population-based retrospective study.Frontiers in medicine · 2025Article
- Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.The journal of physical chemistry. B · 2024Article
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Reused Protein Segments Linked to Functional Dynamics.Molecular biology and evolution · 2024Article
- The "violin model": Looking at community networks for dynamic allostery.The Journal of chemical physics · 2023Review
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins.Biomolecules · 2022Article
- Review
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Study of Allosteric Transitions of Human P-Glycoprotein by Using the Two-State Anisotropic Network Model.Frontiers in medicine · 2022Article
- Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes.International journal of molecular sciences · 2021Article
- "Dividing and Conquering" and "Caching" in Molecular Modeling.International journal of molecular sciences · 2021Review
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.Current opinion in structural biology · 2020Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Elastic networks have been used as simple models of proteins to study their slow structural dynamics. They consist of point-like particles connected by linear Hookean springs and hence are convenient for linear normal mode analysis around a given reference structure. Furthermore, dynamic simulations using these models can provide new insights. As the computational cost associated with these models is considerably lower compared to that of all-atom models, they are also convenient for comparative studies between multiple protein structures. In this review, we introduce examples of coarse-grained molecular dynamics studies using elastic network models and their derivatives, focusing on the nonlinear phenomena, and discuss their applicability to large-scale macromolecular assemblies.
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Registered trials
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