ArticleNature communications2017
Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 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
90 citing papers in PubMed, 190 citations in OpenAlex.
- Atomic resolution structure of human papillomavirus bound to heparin.Nature communications · 2026Article
- Structure-based simulations of the full Flock House virus capsid reveal pathways and energetics of infection-critical peptide externalization.Biophysical journal · 2026Article
- A geometric criterion links HIV-1 capsid topography to its biophysical properties and function.Nature communications · 2026Article
- An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies.Biophysical journal · 2026Article
- Mechanism of HIV-1 Capsid Rupture and Uncoating by Reverse Transcription.bioRxiv : the preprint server for biology · 2026Article
- Role of viral protein ratio in the structure and separation of empty and full adeno-associated virus capsids: A molecular dynamics study.Molecular therapy. Advances · 2026Article
- Stoichiometric binding of Cyclophilin-A to the HIV-1 capsid modulates its mechanoelastic properties.bioRxiv : the preprint server for biology · 2026Article
- Structural organization of HBV pgRNA genome driven by phase separation in capsid confinement.Nature communications · 2026Article
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
- Transient Occupancy and Pore Dynamics: IP6 Behavior in HIV-1The journal of physical chemistry. B · 2026Article
- Computational methods in physical virology: a critical perspective across lengths and timescales.FEMS microbiology reviews · 2026Review
- Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment.The journal of physical chemistry. B · 2025Article
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- IP6, PF74 affect HIV-1 capsid stability through modulation of hexamer-hexamer tilt angle preference.Biophysical journal · 2025Article
- Review
- Review
- Elasticity of the HIV-1 core facilitates nuclear entry and infection.PLoS pathogens · 2024Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Article
- Advancements and Practical Considerations for Biophysical Research: Navigating the Challenges and Future of Super-resolution Microscopy.Chemical & biomedical imaging · 2024Review
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ∼1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.
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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.