ArticleJournal of chemical theory and computation2014
On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- A continuous-space analytical framework for committor functions from molecular dynamics.The Journal of chemical physics · 2026Article
- Metastable Protein-Protein Interactions as a Design Principle for PROTACs: Insights from the RIPK1-VHL System.JACS Au · 2026Article
- Article
- Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A Practical Guide to Transition State Analysis in Biomolecular Simulations with TS-DAR.The journal of physical chemistry. B · 2025Article
- Markovian state models uncover casein kinase 1 dynamics that govern circadian period.Biophysical journal · 2025Article
- Memory kernel minimization-based neural networks for discovering slow collective variables of biomolecular dynamics.Nature computational science · 2025Article
- AMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular Dynamics.Journal of chemical theory and computation · 2025Article
- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space.Nature communications · 2025Article
- Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.The Journal of chemical physics · 2024Article
- Disruption of the FMN-A524 interaction cascade and Glu513-induced collapse of the hydrophobic barrier promotes light-induced Jα-helix unfolding in AsLOV2.Biophysical journal · 2023Article
- Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels.The Journal of chemical physics · 2023Article
- GraphVAMPnets for uncovering slow collective variables of self-assembly dynamics.The Journal of chemical physics · 2023Article
- An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.Journal of chemical theory and computation · 2023Article
- 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
- Automated Path Searching Reveals the Mechanism of Hydrolysis Enhancement by T4 Lysozyme Mutants.International journal of molecular sciences · 2022Article
- Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions.Molecules (Basel, Switzerland) · 2022Review
- Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody.Biomolecules · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Owing to recent developments in computational algorithms and architectures, it is now computationally tractable to explore biologically relevant, equilibrium dynamics of realistically-sized functional proteins using all-atom molecular dynamics simulations. Molecular dynamics simulations coupled with Markov state models is a nascent but rapidly growing technology that is enabling robust exploration of equilibrium dynamics. The objective of this work is to explore the challenges of coupling molecular dynamics simulations and Markov state models in the study of functional proteins. Using recent studies as a framework, we explore progress in sampling, model building, model selection, and coarse-grained analysis of models. Our goal is to highlight some of the current challenges in applying Markov state models to realistically-sized proteins and spur discussion on advances in the field.
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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.