Minimal coarse-grained models for molecular self-organisation in biology
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The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.
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Many modeling techniques needed for a first-pass approximation (e.g., coarse-graining) already exist, requiring proper scaling-up and integration into a self-consistent system.
“Arguably, many modeling techniques needed for a first-pass approximation (e.g. coarse-graining [56–58]) already exist, requiring “just” proper scaling-up and integration into a self-consistent system.”
From Challenges in protein docking (2020) · cites this paper as [58]
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Colì, D., Michieletto, D., Marenduzzo, D., & Orlandini, E. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/379941 · Cited by 1 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [18][18] V. VanBuren, L. Cassimeris, D. J. Odde, Mechanochemical Model of Microtubule Structure and SelfAssembly Kinetics, Biophysical Journal 89 (5) (2005) 2911-2926 -
Cited by
Sorted by citations
Vakser, I. A. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.07.001 · Cited by 62 · see citing works
- Authors
- Hafner, A. E., Krausser, J., & Šarić, A.
- Affiliations
- University College London (GB)
- Corresponding author
- Šarić, Anđela
- Venue
- Current Opinion in Structural Biology
- Publisher
- Elsevier BV
- Published
- 2019-10
- Volume
- 58
- Pages
- 43-52
- ISSN
- 0959-440X (ISSN-L)
- OpenAlex
- W2950563931
- Cited by
- 58
- References
- 103
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 12 · 2023: 4 · 2022: 7 · 2021: 15 · 2020: 8 · 2019: 1
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- green
- arxiv.org
- Locations
- Current Opinion in Structural Biology (publishedVersion)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- arXiv (Cornell University)
- Funders
- Engineering and Physical Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- coarse-grained models, macromolecular complexes, protein assembly, multiscale modeling, molecular machines, disease mechanisms
- MeSH terms
- Humans, Models, Molecular, Genomics, Protein Aggregates
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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