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MSBack: Multiscale Backmapping of Highly Coarse-Grained Proteins Using Constrained Diffusion
Open accessPublished version of a preprint
Abstract
Coarse-grained (CG) molecular dynamics is a powerful tool for simulating the collective behavior of biomolecules. However, the structural information lost during coarse-graining prevents the CG configurations from being more widely useful (e.g., for ligand binding). Regenerating the lost all-atom coordinates, or backmapping, is an unmet challenge for protein CG at resolutions lower than one coarse-grain site or bead per amino acid residue. This low resolution is computationally necessary to simulate many protein complexes including viruses like SARS-CoV-2 and HIV-1. We propose MSBack, a method to backmap highly CG proteins using a diffusion model for the all-atom coordinates constrained to fit the CG coordinates. This diffusion process works by perturbing a known all-atom structure and does not require retraining. We show that this stochastically generates a distribution of α-carbon traces that match the CG coordinates. By combining this with physics-based methods for smaller-length backmapping, we fully backmap a mature HIV-1 capsid bound with the small molecule inositol hexakisphosphate at 1 Å resolution.
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Highly accurate protein structure prediction with AlphaFold
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De novo design of protein structure and function with RFdiffusion
Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2023) · Nature · doi:10.1038/s41586-023-06415-8 · Cited by 2,325
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Metadata
- Authors
- Waltmann, C., Wang, Y., Yang, C., Kim, S., & Voth, G. A.
- Affiliations
- University of Chicago (US)
- Corresponding author
- Voth, Gregory A.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2025-06-02
- Volume
- 21
- Issue
- 12
- Pages
- 6184-6193
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W4410940969
- Cited by
- 11
- References
- 5
- Citations by year
- 2026: 8 · 2025: 3
- FWCI
- 3.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Chemical Theory and Computation (publishedVersion, cc-by-nc-nd)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (F32AI186429, R01AI178850, U54AI170855)
- 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 › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- restricted diffusion, diffusion models, HIV-1 capsid, phytic acid, protein complexes, SARS-CoV-2, ligand binding
- MeSH terms
- SARS-CoV-2, Capsid, Diffusion, Protein Conformation, Proteins, HIV-1, Capsid Proteins, Molecular Dynamics Simulation
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