ArticleJournal of chemical theory and computation2025
MSBack: Multiscale Backmapping of Highly Coarse-Grained Proteins Using Constrained Diffusion.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Enhanced Sampling of Protein Conformations in AlphaFold3 with Repulsive Bias in the Diffusion Generative Model.JACS Au · 2026Article
- Mechanistic Insights into HIV-1 Capsid Interactions with CPSF6.bioRxiv : the preprint server for biology · 2026Article
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.Journal of the American Chemical Society · 2026Article
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.bioRxiv : the preprint server for biology · 2026Article
- Bayesian-Steered Structure Prediction of Mechanical Biomolecules Using Twisted Diffusion.bioRxiv : the preprint server for biology · 2026Article
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Authors and funding
5 authors.
Funding
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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Registered trials
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