ArticleBiophysical journal2009
Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Coarse-grained molecular dynamics simulation of gallic acid delivery using span60-based niosomes.Scientific reports · 2026Article
- MSBack: Multiscale Backmapping of Highly Coarse-Grained Proteins Using Constrained Diffusion.Journal of chemical theory and computation · 2025Article
- Generating Protein Structures for Pathway Discovery Using Deep Learning.Journal of chemical theory and computation · 2024Article
- Article
- Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining.Nature communications · 2023Article
- Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022Review
- Building an extensible cell wall.Plant physiology · 2022Article
- 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
- 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
- Coarse-Grained Simulation of Mechanical Properties of Single Microtubules With Micrometer Length.Frontiers in molecular biosciences · 2020Article
- A deep learning approach to the structural analysis of proteins.Interface focus · 2019Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Optimizing model representation for integrative structure determination of macromolecular assemblies.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- Highly Coarse-Grained Representations of Transmembrane Proteins.Journal of chemical theory and computation · 2017Article
- Steric exclusion and constraint satisfaction in multi-scale coarse-grained simulations.Computational biology and chemistry · 2016Article
- Modeling Functional Motions of Biological Systems by Customized Natural Moves.Biophysical journal · 2016Article
- Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.PLoS computational biology · 2015Article
- Sequence, structure, and cooperativity in folding of elementary protein structural motifs.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coarse-grained (CG) models of large biomolecular complexes enable simulations of these systems over long timescales that are not accessible for atomistic molecular dynamics (MD) simulations. A systematic methodology, called essential dynamics coarse-graining (ED-CG), has been developed for defining coarse-grained sites in a large biomolecule. The method variationally determines the CG sites so that key dynamic domains in the protein are preserved in the CG representation. The original ED-CG method relies on a principal component analysis (PCA) of a MD trajectory. However, for many large proteins and multi-protein complexes such an analysis may not converge or even be possible. This work develops a new ED-CG scheme using an elastic network model (ENM) of the protein structure. In this procedure, the low-frequency normal modes obtained by ENM are used to define dynamic domains and to define the CG representation accordingly. The method is then applied to several proteins, such as the HIV-1 CA protein dimer, ATP-bound G-actin, and the Arp2/3 complex. Numerical results show that ED-CG with ENM (ENM-ED-CG) is much faster than ED-CG with PCA because no MD is necessary. The ENM-ED-CG models also capture functional essential dynamics of the proteins almost as well as those using full MD with PCA. Therefore, the ENM-ED-CG method may be better suited to coarse-grain a very large biomolecule or biomolecular complex that is too computationally expensive to be simulated by conventional MD, or when a high resolution atomic structure is not even available.
Indexed as
Identifiers
What OpenQuestion holds
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.