ArticlePLoS computational biology2013
Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells.Bioinformatics (Oxford, England) · 2024Article
- Review
- The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids.Frontiers in molecular biosciences · 2022Article
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules.Journal of chemical theory and computation · 2020Article
- Ligand-protein interactions in lysozyme investigated through a dual-resolution model.Proteins · 2020Article
- Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis.PLoS computational biology · 2020Article
- Surface stresses in complex viral capsids and non-quasi-equivalent viral architectures.Journal of the Royal Society, Interface · 2020Article
- Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2020Article
- A deep learning approach to the structural analysis of proteins.Interface focus · 2019Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.Scientific reports · 2018Article
- Molecular jenga: the percolation phase transition (collapse) in virus capsids.Physical biology · 2018Article
- Molecular dynamics study of T = 3 capsid assembly.Journal of biological physics · 2018Article
- Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids.Frontiers in molecular biosciences · 2016Article
- Article
- Molecular dynamics simulations of large macromolecular complexes.Current opinion in structural biology · 2015Review
- Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses.Biophysical journal · 2015Article
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Authors and funding
6 authors.
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Abstract
Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available.
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