ArticleThe Journal of chemical physics2016
Markov state models of protein misfolding.
Article in The Journal of chemical physics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 38 citations in OpenAlex.
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins.The journal of physical chemistry. B · 2022Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CLJournal of biomolecular structure & dynamics · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas.PloS one · 2020Article
- Detecting early stage structural changes in wild type, pathogenic and non-pathogenic prion variants using Markov state model.RSC advances · 2019Article
- Direct Learning Hidden Excited State Interaction Patterns from ab initio Dynamics and Its Implication as Alternative Molecular Mechanism Models.Scientific reports · 2017Article
- Optimized parameter selection reveals trends in Markov state models for protein folding.The Journal of chemical physics · 2016Article
- Structural Determinants of Misfolding in Multidomain Proteins.PLoS computational biology · 2016Article
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Authors and funding
3 authors at 1 institution in 3 countries.
Funding
Abstract
Markov state models (MSMs) are an extremely useful tool for understanding the conformational dynamics of macromolecules and for analyzing MD simulations in a quantitative fashion. They have been extensively used for peptide and protein folding, for small molecule binding, and for the study of native ensemble dynamics. Here, we adapt the MSM methodology to gain insight into the dynamics of misfolded states. To overcome possible flaws in root-mean-square deviation (RMSD)-based metrics, we introduce a novel discretization approach, based on coarse-grained contact maps. In addition, we extend the MSM methodology to include "sink" states in order to account for the irreversibility (on simulation time scales) of processes like protein misfolding. We apply this method to analyze the mechanism of misfolding of tandem repeats of titin domains, and how it is influenced by confinement in a chaperonin-like cavity.
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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.