ArticleNature communications2023
Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- Stoichiometric binding of Cyclophilin-A to the HIV-1 capsid modulates its mechanoelastic properties.bioRxiv : the preprint server for biology · 2026Article
- Membrane bending energy selects for compact growth of protein assemblies.bioRxiv : the preprint server for biology · 2025Article
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- MIL-53(Fe)-Glucose self-assembled complex for enhanced angiogenesis and endothelial tip cell activation.Journal of nanobiotechnology · 2025Article
- Elasticity of the HIV-1 core facilitates nuclear entry and infection.PLoS pathogens · 2024Article
- Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses.Sub-cellular biochemistry · 2024Review
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches.Biochemical Society transactions · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.
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.