Analysis of protein folding simulation with moving root mean square deviation
We apply moving root-mean-square deviation (mRMSD), which does not require a reference
structure, as a method for analyzing protein dynamics. This method can be used to calculate …
structure, as a method for analyzing protein dynamics. This method can be used to calculate …
Broad distributions of transition-path times are fingerprints of multidimensionality of the underlying free energy landscapes
R Satija, AM Berezhkovskii… - Proceedings of the …, 2020 - National Acad Sciences
Recent single-molecule experiments have observed transition paths, ie, brief events where
molecules (particularly biomolecules) are caught in the act of surmounting activation …
molecules (particularly biomolecules) are caught in the act of surmounting activation …
[HTML][HTML] Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding
Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions
of proteins in atomistic detail. However, the accuracy of models derived from simulations …
of proteins in atomistic detail. However, the accuracy of models derived from simulations …
[HTML][HTML] Relaxation mode analysis for molecular dynamics simulations of proteins
A Mitsutake, H Takano - Biophysical Reviews, 2018 - Springer
Molecular dynamics simulation is a powerful method for investigating the structural stability,
dynamics, and function of biopolymers at the atomic level. In recent years, it has become …
dynamics, and function of biopolymers at the atomic level. In recent years, it has become …
Size-and-shape space gaussian mixture models for structural clustering of molecular dynamics trajectories
Determining the optimal number and identity of structural clusters from an ensemble of
molecular configurations continues to be a challenge. Recent structural clustering methods …
molecular configurations continues to be a challenge. Recent structural clustering methods …
Generalized Langevin equation as a model for barrier crossing dynamics in biomolecular folding
R Satija, DE Makarov - The Journal of Physical Chemistry B, 2019 - ACS Publications
Conformational memory in single-molecule dynamics has attracted recent attention and, in
particular, has been invoked as a possible explanation of some of the intriguing properties of …
particular, has been invoked as a possible explanation of some of the intriguing properties of …
[HTML][HTML] Transition path times reveal memory effects and anomalous diffusion in the dynamics of protein folding
Recent single-molecule experiments probed transition paths of biomolecular folding and, in
particular, measured the time biomolecules spend while crossing their free energy barriers …
particular, measured the time biomolecules spend while crossing their free energy barriers …
Barrier crossing dynamics from single-molecule measurements
DE Makarov - The Journal of Physical Chemistry B, 2021 - ACS Publications
Chemists visualize chemical reactions as motion along one-dimensional “reaction
coordinates” over free energy barriers. Various rate theories, such as transition state theory …
coordinates” over free energy barriers. Various rate theories, such as transition state theory …
Transition path times in non-Markovian activated rate processes
E Medina, R Satija, DE Makarov - The Journal of Physical …, 2018 - ACS Publications
Transition paths are brief excursions taken by molecules when they cross barriers
separating stable molecular conformations. When observed in single-molecule experiments …
separating stable molecular conformations. When observed in single-molecule experiments …
[HTML][HTML] Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders
Conformational sampling of biomolecules using molecular dynamics simulations often
produces a large amount of high dimensional data that makes it difficult to interpret using …
produces a large amount of high dimensional data that makes it difficult to interpret using …