ArticleJournal of chemical information and modeling2025
Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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
6 citing papers in PubMed.
- Extracellular Vesicle-Bound Bacterial Toxin Pneumolysin Triggers Membrane Engagement and Damage Beyond Canonical Pore Formation.Journal of extracellular vesicles · 2026Article
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior.ACS central science · 2025Article
- TS2CG as a Membrane Builder.Journal of chemical theory and computation · 2025Article
- A Membrane-Disruptive Action of VBIT-4 Challenges Its Role as a Widely Used VDAC Oligomerization Inhibitor.bioRxiv : the preprint server for biology · 2025Article
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current trends in molecular modeling are geared toward increasingly realistic representations of the biological environments reflected in larger, more complex systems. The complexity of the system-building procedure is ideally handled by software that converts user-provided descriptors into system coordinates. This, however, is not a trivial task, as building algorithms use simplifications that result in inaccuracies in the system properties. We created COBY, a coarse-grained system builder that can create a large variety of systems in a single command call with an improved accuracy of the complex membrane and solvent building procedures. COBY also contains features for building diverse systems in a single step, and has functionalities aiding force field development. COBY is an open-source software written in Python 3, and the code, documentation, and tutorials are hosted at https://github.com/MikkelDA/COBY.
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Identifiers
What Socratic 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 Socratic graph.