ArticleFaraday discussions2014
3D molecular models of whole HIV-1 virions generated with cellPACK.
Article in Faraday discussions, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed, 66 citations in OpenAlex.
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- Mol* web molecular graphics engine.Protein science : a publication of the Protein Society · 2026Article
- A Cell Metamodel Uncovers Mechanistic Drivers of Disease Phenotypes Across Molecular, Cellular, and Tissue Scales.Research square · 2025Article
- HIV capsids: orchestrators of innate immune evasion, pathogenesis and pandemicity.The Journal of general virology · 2025Review
- Mesoscale explorer: Visual exploration of large-scale molecular models.Protein science : a publication of the Protein Society · 2024Article
- Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models.bioRxiv : the preprint server for biology · 2024Article
- CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.Nature communications · 2024Article
- CHARMM-GUIJournal of chemical theory and computation · 2023Review
- ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses.bioRxiv : the preprint server for biology · 2022Article
- Assembly and Analysis of Cell-Scale Membrane Envelopes.Journal of chemical information and modeling · 2022Article
- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
- Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API.Journal of chemical information and modeling · 2021Article
- Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- New and notable: A multiscale coarse-grained model of the SARS-CoV-2 virion.Biophysical journal · 2021Article
- High-performance macromolecular data delivery and visualization for the web.Acta crystallographica. Section D, Structural biology · 2020Article
- Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation.MolVa : Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020 · 2020Article
- AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.Journal of computational chemistry · 2019Article
- Mathematical determination of the HIV-1 matrix shell structure and its impact on the biology of HIV-1.PloS one · 2019Article
- Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments.IEEE transactions on visualization and computer graphics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology.
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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.