RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
Markov state models to study the functional dynamics of proteins in the wake of machine learning
Markov state models (MSMs) based on molecular dynamics (MD) simulations are routinely
employed to study protein folding, however, their application to functional conformational …
employed to study protein folding, however, their application to functional conformational …
PyEMMA 2: A software package for estimation, validation, and analysis of Markov models
MK Scherer, B Trendelkamp-Schroer… - Journal of chemical …, 2015 - ACS Publications
Markov (state) models (MSMs) and related models of molecular kinetics have recently
received a surge of interest as they can systematically reconcile simulation data from either …
received a surge of interest as they can systematically reconcile simulation data from either …
An efficient path classification algorithm based on variational autoencoder to identify metastable path channels for complex conformational changes
Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …
play important roles in many chemical and biological processes. Constructing the Markov …
Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules
The function of complex biomolecular machines relies heavily on their conformational
changes. Investigating these functional conformational changes is therefore essential for …
changes. Investigating these functional conformational changes is therefore essential for …
Biogenesis and function of ago-associated RNAs
I Daugaard, TB Hansen - Trends in genetics, 2017 - cell.com
Numerous sophisticated high-throughput sequencing technologies have been developed
over the past decade, and these have enabled the discovery of a diverse catalog of small …
over the past decade, and these have enabled the discovery of a diverse catalog of small …
Modelling proteins' hidden conformations to predict antibiotic resistance
TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves
activity against new drugs. However, functional changes are not easily explained by …
activity against new drugs. However, functional changes are not easily explained by …
GraphVAMPnets for uncovering slow collective variables of self-assembly dynamics
Uncovering slow collective variables (CVs) of self-assembly dynamics is important to
elucidate its numerous kinetic assembly pathways and drive the design of novel structures …
elucidate its numerous kinetic assembly pathways and drive the design of novel structures …
Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model
To initiate transcription, the holoenzyme (RNA polymerase [RNAP] in complex with σ factor)
loads the promoter DNA via the flexible loading gate created by the clamp and β-lobe, yet …
loads the promoter DNA via the flexible loading gate created by the clamp and β-lobe, yet …
Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels
The generalized master equation (GME) provides a powerful approach to study
biomolecular dynamics via non-Markovian dynamic models built from molecular dynamics …
biomolecular dynamics via non-Markovian dynamic models built from molecular dynamics …