Modeling Viral Capsid Assembly: A Review of Computational Strategies and Applications

Abstract

Viral capsid assembly is a complex and critical process, essential for understanding viral behavior, evolution, and the development of antiviral treatments, vaccines, and nanotechnology. Significant progress in studying viral capsid assembly has been achieved through various computational approaches, including molecular dynamics (MD) simulations, stochastic dynamics simulations, coarse-grained (CG) models, electrostatic analyses, lattice models, hybrid techniques, machine learning methods, and kinetic models. Each of these techniques offers unique advantages, and by integrating these diverse computational strategies, researchers can more accurately model the dynamic behaviors and structural features of viral capsids, deepening our understanding of the assembly process. This review provides a comprehensive overview of studies on viral capsid assembly, emphasizing their critical role in advancing our knowledge. It examines the contributions, strengths, and limitations of different computational methods, presents key computational works in the field, and analyzes milestone studies that have shaped current research.

Keywords: coarse-grained models; computational methods; molecular dynamics simulations; viral capsid assembly.

Figure 1

Computational approaches for understanding viral capsid assembly.

Figure 2

The schematic illustration of the coarse-grained models.

Figure 3

The schematic illustration of electric field lines at the binding interfaces of capsomers. The density of the electrostatic field lines indicates the strength of the electrostatic interactions between capsomers.