ArticleThe Journal of chemical physics2014
Using Markov state models to study self-assembly.
Article in The Journal of chemical physics, 2014. 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.
- Modeling Reveals How Direct-Acting Antivirals Redirect HBV Capsid Assembly Pathways to Noninfectious Products.bioRxiv : the preprint server for biology · 2026Article
- Coarse-Graining Self-Assembly by the Stochastic Landscape Method.Journal of chemical theory and computation · 2025Article
- Temporal control by cofactors prevents kinetic trapping in retroviral Gag lattice assembly.Biophysical journal · 2023Article
- Optimization of non-equilibrium self-assembly protocols using Markov state models.The Journal of chemical physics · 2022Article
- Article
- Physics of viral dynamics.Nature reviews. Physics · 2021Review
- Should Virus Capsids Assemble Perfectly? Theory and Observation of Defects.Biophysical journal · 2020Article
- Evolution of Intermediates during Capsid Assembly of Hepatitis B Virus with Phenylpropenamide-Based Antivirals.ACS infectious diseases · 2019Article
- Universal folding pathways of polyhedron nets.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The role of multivalency in the association kinetics of patchy particle complexes.The Journal of chemical physics · 2017Article
- Chemical and entropic control on the molecular self-assembly process.Nature communications · 2017Article
- Reaction-diffusion basis of retroviral infectivity.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2016Article
- Allosteric Control of Icosahedral Capsid Assembly.The journal of physical chemistry. B · 2016Article
- State-space reduction and equivalence class sampling for a molecular self-assembly model.Royal Society open science · 2016Article
- Recent advances in coarse-grained modeling of virus assembly.Current opinion in virology · 2016Review
- Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.The Journal of chemical physics · 2015Article
- Mechanisms of virus assembly.Annual review of physical chemistry · 2015Review
- Pathways for virus assembly around nucleic acids.Journal of molecular biology · 2014Article
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Authors and funding
2 authors.
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Abstract
Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to construct MSMs that is applicable to modeling a broad class of multi-molecular assembly reactions. Distinct structures formed during assembly are distinguished by their undirected graphs, which are defined by strong subunit interactions. Spatial inhomogeneities of free subunits are accounted for using a recently developed Gaussian-based signature. Simplifications to this state identification are also investigated. The feasibility of this approach is demonstrated on two different coarse-grained models for virus self-assembly. We find good agreement between the dynamics predicted by the MSMs and long, unbiased simulations, and that the MSMs can reduce overall simulation time by orders of magnitude.
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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.