ReviewCurrent opinion in structural biology2014
Markov state models of biomolecular conformational dynamics.
Review in Current opinion in structural biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 303 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
303 citing papers in PubMed.
- Kinetic, computational, and phylogenetic characterisation of PA2125 from Pseudomonas aeruginosa PAO1: a hydroxybenzaldehyde dehydrogenase of the newly defined ALDH33 family.Bioscience reports · 2026Article
- Enhanced Sampling of Protein Conformations in AlphaFold3 with Repulsive Bias in the Diffusion Generative Model.JACS Au · 2026Article
- A Simulation-Free Topological Basis for Building Compact Koopman Models of Protein Folding.Journal of chemical information and modeling · 2026Article
- Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.Journal of chemical theory and computation · 2026Article
- Allosteric Gating Mechanism Regulates Odorant Selectivity and Antagonism in Odorant Receptors.bioRxiv : the preprint server for biology · 2026Article
- Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.Journal of biological physics · 2026Review
- Article
- Bridging Atomistic and Mesoscale Lithium Transport via Machine-Learned Force Fields and Markov State Models.Journal of chemical theory and computation · 2026Article
- Elucidating the Structure and Activation Mechanisms of GPCRs Using Modern Computational and AI Tools.Cell biochemistry and biophysics · 2026Review
- Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways.Journal of chemical theory and computation · 2026Article
- A Hydrophobic Cluster Modulates Long-Range Allostery in the TRMT2A RNA Recognition Motif.Journal of chemical information and modeling · 2026Article
- Integrative Computational Chemistry Approaches in Modern Drug Discovery: Advances in Docking, Pharmacophore Modeling, Molecular Dynamics, and Virtual Screening.Pharmaceutics · 2026Review
- Conformational Dynamics of NaJournal of chemical information and modeling · 2026Article
- Succession-diagram-based Markov chains reveal the attractor landscape of asynchronous Boolean networks.NPJ systems biology and applications · 2026Article
- Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data.bioRxiv : the preprint server for biology · 2026Article
- Molecular Modeling of the Pathogenetic Mechanisms of Neuropsychiatric Disorders.International journal of molecular sciences · 2026Review
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Free Energy Calculation Method Based on Enhanced Sampling of Diverse Protein Conformations Predicted by Artificial Intelligence.The journal of physical chemistry letters · 2026Article
- Article
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
243 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
It has recently become practical to construct Markov state models (MSMs) that reproduce the long-time statistical conformational dynamics of biomolecules using data from molecular dynamics simulations. MSMs can predict both stationary and kinetic quantities on long timescales (e.g. milliseconds) using a set of atomistic molecular dynamics simulations that are individually much shorter, thus addressing the well-known sampling problem in molecular dynamics simulation. In addition to providing predictive quantitative models, MSMs greatly facilitate both the extraction of insight into biomolecular mechanism (such as folding and functional dynamics) and quantitative comparison with single-molecule and ensemble kinetics experiments. A variety of methodological advances and software packages now bring the construction of these models closer to routine practice. Here, we review recent progress in this field, considering theoretical and methodological advances, new software tools, and recent applications of these approaches in several domains of biochemistry and biophysics, commenting on remaining challenges.
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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.