Advances in coarse-grained modeling of macromolecular complexes
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Recent progress in coarse-grained (CG) molecular modeling and simulation has facilitated an influx of computational studies on biological macromolecules and their complexes. Given the large separation of length-scales and time-scales that dictate macromolecular biophysics, CG modeling and simulation are well-suited to bridge the microscopic and mesoscopic or macroscopic details observed from all-atom molecular simulations and experiments, respectively. In this review, we first summarize recent innovations in the development of CG models, which broadly include structure-based, knowledge-based, and dynamics-based approaches. We then discuss recent applications of different classes of CG models to explore various macromolecular complexes. Finally, we conclude with an outlook for the future in this ever-growing field of biomolecular modeling.
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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 [57]
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References 102 · Cited by 145
- Authors
- Pak, A. J., & Voth, G. A.
- Affiliations
- University of Chicago (US)
- Corresponding author
- Voth, Gregory A
- Venue
- Current Opinion in Structural Biology
- Publisher
- Elsevier BV
- Published
- 2018-10
- Volume
- 52
- Pages
- 119-126
- ISSN
- 0959-440X (ISSN-L)
- PMC
- PMC6296860
- OpenAlex
- W2902461580
- Cited by
- 145
- References
- 102
- Citations by year
- 2026: 14 · 2025: 14 · 2024: 22 · 2023: 22 · 2022: 16 · 2021: 26 · 2020: 16 · 2019: 14 · 2018: 1
- FWCI
- 1.40
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Current Opinion in Structural Biology (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences of the National Institutes of Health (P50-GM082545)
- National Science Foundation (CHE-1465248)
- Ruth L. Kirschstein National Research Service Award Postdoctoral Fellowship (F32-GM125218)
- 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, biomolecular modeling, protein-protein interaction, biomolecular simulation
- MeSH terms
- Models, Molecular, Molecular Conformation, Macromolecular Substances, Molecular Dynamics Simulation
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