ReviewBiochimica et biophysica acta2016
Computational virology: From the inside out.
Review in Biochimica et biophysica acta, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- A hybrid framework of generative deep learning for antiviral peptide discovery.Scientific reports · 2025Article
- Review
- The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus.Vaccines · 2022Review
- Model architectures for bacterial membranes.Biophysical reviews · 2022Review
- Molecular dynamics of the viral life cycle: progress and prospects.Current opinion in virology · 2021Review
- Canine Morbillivirus from Colombian Lineage Exhibits In Silico and In Vitro Potential to Infect Human Cells.Pathogens (Basel, Switzerland) · 2021Article
- Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus.Biophysical journal · 2021Article
- Computational modelling of flavivirus dynamics: The ins and outs.Methods (San Diego, Calif.) · 2021Review
- Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations.The Journal of chemical physics · 2020Article
- Forecasting the timeframe of 2019-nCoV and human cells interaction with reverse engineering.Progress in biophysics and molecular biology · 2020Review
- Coronavirus through Delaware's Computational Microscope.Delaware journal of public health · 2020Article
- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities.Journal of chemical information and modeling · 2019Article
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- All-atom virus simulations.Current opinion in virology · 2018Review
- The unequivocal preponderance of biocomputation in clinical virology.RSC advances · 2018Review
- Instant Construction and Visualization of Crowded Biological Environments.IEEE transactions on visualization and computer graphics · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
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.
Funding
Abstract
Viruses typically pack their genetic material within a protein capsid. Enveloped viruses also have an outer membrane made up of a lipid bilayer and membrane-spanning glycoproteins. X-ray diffraction and cryoelectron microscopy provide high resolution static views of viral structure. Molecular dynamics (MD) simulations may be used to provide dynamic insights into the structures of viruses and their components. There have been a number of simulations of viral capsids and (in some cases) of the inner core of RNA or DNA packaged within them. These simulations have generally focussed on the structural integrity and stability of the capsid and/or on the influence of the nucleic acid core on capsid stability. More recently there have been a number of simulation studies of enveloped viruses, including HIV-1, influenza A, and dengue virus. These have addressed the dynamic behaviour of the capsid, the matrix, and/or of the outer envelope. Analysis of the dynamics of the lipid bilayer components of the envelopes of influenza A and of dengue virus reveals a degree of biophysical robustness, which may contribute to the stability of virus particles in different environments. Significant computational challenges need to be addressed to aid simulation of complex viruses and their membranes, including the need to integrate structural data from a range of sources to enable us to move towards simulations of intact virions. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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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.