ArticleJournal of chemical theory and computation2019
Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Mapping Still Matters: Coarse-Graining with Machine Learning Potentials.Journal of chemical information and modeling · 2026Article
- Optimizing a coarse-grained model for large-scale membrane protein simulation.Biophysical reports · 2025Article
- Machine Learning Approaches in Soft Matter Molecular Simulation and Materials Characterization: Challenges and Perspectives.ChemPlusChem · 2025Article
- Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins.Journal of chemical information and modeling · 2023Article
- Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics.ACS central science · 2023Article
- 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
- A Deep Graph Network-Enhanced Sampling Approach to Efficiently Explore the Space of Reduced Representations of Proteins.Frontiers in molecular biosciences · 2021Article
- A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules.The European physical journal. B · 2021Article
- An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules.Journal of chemical theory and computation · 2020Article
- Ligand-protein interactions in lysozyme investigated through a dual-resolution model.Proteins · 2020Article
- Exploring the landscape of model representations.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A deep learning approach to the structural analysis of proteins.Interface focus · 2019Article
- Optimizing model representation for integrative structure determination of macromolecular assemblies.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low computational cost. Their efficiency and effectiveness have made them a pivotal instrument in the computer-aided study of proteins and, since a few years, also of nucleic acids. In general, the coarse-grained sites, i.e. those effective force centers onto which the all-atom structure is mapped, are constructed based on intuitive rules: a typical choice for proteins is to retain only the C
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