ArticleNature methods2015
cellPACK: a virtual mesoscope to model and visualize structural systems biology.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 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
86 citing papers in PubMed, 160 citations in OpenAlex.
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- Understanding chemical reactions through multimedia resolution data artistic educational tool (MRDAET).Protein science : a publication of the Protein Society · 2026Article
- Cellular and molecular representations: Following the lesson of David Goodsell.Protein science : a publication of the Protein Society · 2026Article
- The evolving landscape of molecular visualization.Protein science : a publication of the Protein Society · 2026Review
- The virus lesson: Teaching viral structure and quasi-symmetry in mixed reality.Protein science : a publication of the Protein Society · 2026Article
- Compartment-guided assembly of large-scale molecular models with Bentopy.Protein science : a publication of the Protein Society · 2026Article
- Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities.Briefings in bioinformatics · 2026Review
- A Cell Metamodel Uncovers Mechanistic Drivers of Disease Phenotypes Across Molecular, Cellular, and Tissue Scales.Research square · 2025Article
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- Interpretable representation learning for 3D multi-piece intracellular structures using point clouds.Nature methods · 2025Article
- Enabling Atomistic Modeling and Simulation of Complex Curved Cellular Membranes with xMAS Builder.bioRxiv : the preprint server for biology · 2025Article
- From Gene to Whole Cell: Modeling, Visualization, and Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- Foundations of a Compositional Systems Biology.ArXiv · 2024Article
- 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
- Overlay databank unlocks data-driven analyses of biomolecules for all.Nature communications · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- The Role of Technical Directors on a 3D Animation Team: Viewpoint and Professional Insight.The Journal of biocommunication · 2024Review
26 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
6 authors at 1 institution in 1 country.
Funding
Abstract
cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is available as open-source code, with tools for validation of models and with 'recipes' and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org/.
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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.