ArticleThe Journal of chemical physics2014
Perspective: Markov models for long-timescale biomolecular dynamics.
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 33 papers.
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Who cites it
33 citing papers in PubMed.
- DreamFold: A World Model to efficiently generate protein folding pathways in the latent space.Protein science : a publication of the Protein Society · 2026Article
- Approximate matrix exponential: a fast and accurate solver for Markov kinetic models of ion channels.Frontiers in computational neuroscience · 2026Article
- Symmetry-adapted Markov state models of closing, opening, and desensitizing in α 7 nicotinic acetylcholine receptors.Nature communications · 2024Article
- The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition.Communications biology · 2024Article
- Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Optimization of non-equilibrium self-assembly protocols using Markov state models.The Journal of chemical physics · 2022Article
- Estradiol induces allosteric coupling and partitioning of sex-hormone-binding globulin monomers among conformational states.iScience · 2021Article
- The Two-Step Clustering Approach for Metastable States Learning.International journal of molecular sciences · 2021Review
- Biomolecular modeling thrives in the age of technology.Nature computational science · 2021Article
- MD Simulations on a Well-Built Docking Model Reveal Fine Mechanical Stability and Force-Dependent Dissociation of Mac-1/GPIbα Complex.Frontiers in molecular biosciences · 2021Article
- Integrated Variational Approach to Conformational Dynamics: A Robust Strategy for Identifying Eigenfunctions of Dynamical Operators.The journal of physical chemistry. B · 2020Article
- Enzyme dynamics: Looking beyond a single structure.ChemCatChem · 2020Article
- Data-Driven Molecular Dynamics: A Multifaceted Challenge.Pharmaceuticals (Basel, Switzerland) · 2020Review
- Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating.PLoS computational biology · 2020Article
- A Time-Dependent Quantum Approach to Allostery and a Comparison With Light-Harvesting in Photosynthetic Phenomenon.Frontiers in molecular biosciences · 2020Article
- Galerkin approximation of dynamical quantities using trajectory data.The Journal of chemical physics · 2019Article
- Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory.Biophysics and physicobiology · 2019Review
- Molecular Dynamics Simulation for All.Neuron · 2018Review
- Relaxation mode analysis for molecular dynamics simulations of proteins.Biophysical reviews · 2018Review
- Atomistic Insights into Structural Differences between E3 and E4 Isoforms of Apolipoprotein E.Biophysical journal · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.
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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.