All-atom virus simulations to tackle airborne disease

Abigail C Dommer; Nicholas A Wauer; Siewert J Marrink; Rommie E Amaro

doi:10.1016/j.sbi.2025.103048

All-atom virus simulations to tackle airborne disease

Abigail C Dommer, Nicholas A Wauer, Siewert J Marrink, Rommie E Amaro^*

^*Corresponding author for this work

Molecular Dynamics

Research output: Contribution to journal › Review article › peer-review

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Abstract

We briefly review the latest computational studies focused on modeling viruses with classical all-atom (AA) molecular dynamics. We report on the challenges, current solutions, and ongoing developments in constructing and simulating whole viruses, and discuss unique insights derived from AA mesoscale simulations that cannot be achieved by other means. Finally, we present new opportunities in computational virology to understand viral aerostability within the context of respiratory disease transmission. Overall, we highlight the value of large-scale AA simulation and champion the need for increased interdisciplinary collaboration to generate novel insights and guide future research in respiratory disease.

Original language	English
Article number	103048
Number of pages	11
Journal	Current Opinion in Structural Biology
Volume	92
DOIs	https://doi.org/10.1016/j.sbi.2025.103048
Publication status	Published - Jun-2025

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title = "All-atom virus simulations to tackle airborne disease",

abstract = "We briefly review the latest computational studies focused on modeling viruses with classical all-atom (AA) molecular dynamics. We report on the challenges, current solutions, and ongoing developments in constructing and simulating whole viruses, and discuss unique insights derived from AA mesoscale simulations that cannot be achieved by other means. Finally, we present new opportunities in computational virology to understand viral aerostability within the context of respiratory disease transmission. Overall, we highlight the value of large-scale AA simulation and champion the need for increased interdisciplinary collaboration to generate novel insights and guide future research in respiratory disease.",

author = "Dommer, {Abigail C} and Wauer, {Nicholas A} and Marrink, {Siewert J} and Amaro, {Rommie E}",

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AU - Dommer, Abigail C

AU - Wauer, Nicholas A

AU - Marrink, Siewert J

AU - Amaro, Rommie E

PY - 2025/6

Y1 - 2025/6

N2 - We briefly review the latest computational studies focused on modeling viruses with classical all-atom (AA) molecular dynamics. We report on the challenges, current solutions, and ongoing developments in constructing and simulating whole viruses, and discuss unique insights derived from AA mesoscale simulations that cannot be achieved by other means. Finally, we present new opportunities in computational virology to understand viral aerostability within the context of respiratory disease transmission. Overall, we highlight the value of large-scale AA simulation and champion the need for increased interdisciplinary collaboration to generate novel insights and guide future research in respiratory disease.

AB - We briefly review the latest computational studies focused on modeling viruses with classical all-atom (AA) molecular dynamics. We report on the challenges, current solutions, and ongoing developments in constructing and simulating whole viruses, and discuss unique insights derived from AA mesoscale simulations that cannot be achieved by other means. Finally, we present new opportunities in computational virology to understand viral aerostability within the context of respiratory disease transmission. Overall, we highlight the value of large-scale AA simulation and champion the need for increased interdisciplinary collaboration to generate novel insights and guide future research in respiratory disease.

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DO - 10.1016/j.sbi.2025.103048

M3 - Review article

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SN - 0959-440X

VL - 92

JO - Current Opinion in Structural Biology

JF - Current Opinion in Structural Biology

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All-atom virus simulations to tackle airborne disease

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