Identifying metastable states of folding proteins

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The Protein Folding Network

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Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study

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Dihedral angle principal component analysis of molecular dynamics simulations.

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Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

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Experimental Tests of Villin Subdomain Folding Simulations

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Markov state models based on milestoning

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Protein folded states are kinetic hubs

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Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis.

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Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece.

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Full correlation analysis of conformational protein dynamics

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Comparing geometric and kinetic cluster algorithms for molecular simulation data

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How Complex Is the Dynamics of Peptide Folding?

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One-Dimensional Barrier-Preserving Free-Energy Projections of a β-sheet Miniprotein: New Insights into the Folding Process

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Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

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Protein dynamics investigated by inherent structure analysis

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Going beyond Clustering in MD Trajectory Analysis: An Application to Villin Headpiece Folding

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Large-Scale Context in Protein Folding: Villin Headpiece

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An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles.

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Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

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Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

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Partition of networks into basins of attraction

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Local Transition Gradients Indicating the Global Attributes of Protein Energy Landscapes

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Markov state models of biomolecular conformational dynamics

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Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates.

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Perspective: Identification of collective variables and metastable states of protein dynamics.

Sittel, F., & Stock, G. (2018) · Journal of Chemical Physics · doi:10.1063/1.5049637 · Cited by 137 · see citing works

Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

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Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning

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Contact- and distance-based principal component analysis of protein dynamics.

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Robust Density-Based Clustering To Identify Metastable Conformational States of Proteins.

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Machine Learning of Biomolecular Reaction Coordinates.

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Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

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Folding Dynamics of the Trp-Cage Miniprotein: Evidence for a Native-Like Intermediate from Combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations

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Time-resolved observation of protein allosteric communication

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Principal component analysis on a torus: Theory and application to protein dynamics.

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Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

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Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

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Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes

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Machine Learning for Molecular Dynamics on Long Timescales

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Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models

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Quantitative comparison of alternative methods for coarse-graining biological networks

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Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge

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Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders

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Hierarchical Folding Free Energy Landscape of HP35 Revealed by Most Probable Path Clustering

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Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems

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Identification and Validation of Reaction Coordinates Describing Protein Functional Motion: Hierarchical Dynamics of T4 Lysozyme.

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Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models

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Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories

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A Square Root Approximation of Transition Rates for a Markov State Model

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Dynamical coring of Markov state models.

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Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics

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Protein Function Analysis through Machine Learning

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An Information Bottleneck Approach for Markov Model Construction

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Selecting Features for Markov Modeling: A Case Study on HP35.

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Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its Cα Carbons

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Toward a Benchmark for Markov State Models: The Folding of HP35.

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Markov State Models: To Optimize or Not to Optimize

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Soliton driven relaxation dynamics and protein collapse in the villin headpiece

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Sapphire -Based Clustering

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Coarse-grained conformational surface hopping: Methodology and transferability

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Modeling non-Markovian data using Markov state and Langevin models

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MSMPathfinder: Identification of Pathways in Markov State Models

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Comprehensive and Accurate Ab Initio Energy Surface of Simple Alanine Peptides

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RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics

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Conformational fluctuations in the molten globule state of α-lactalbumin

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Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands

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Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms

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The Role of Conformational Entropy in the Determination of Structural-Kinetic Relationships for Helix-Coil Transitions

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Computational Spectroscopy Tools for Molecular Structure Analysis

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A Probabilistic Framework for Constructing Temporal Relations in Replica Exchange Molecular Trajectories

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Combining multi-scale modelling methods to decipher molecular motions of a branching sucrase from glycoside-hydrolase family 70

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GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation

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Revealing Free Energy Landscape From MD Data via Conditional Angle Partition Tree

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The Two-Step Clustering Approach for Metastable States Learning

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Analysis of dynamically stable patterns in a maze-like corridor using the Wasserstein metric

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Markov-Type State Models to Describe Non-Markovian Dynamics

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Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

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Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics

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Unveiling hidden intermediate states in protein folding with AI-based conditional transition clustering

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Maximum Margin Clustering for State Decomposition of Metastable Systems

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GRadient Adaptive Decomposition (GRAD) Method: Optimized Refinement Along Macrostate Borders in Markov State Models

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