Markov state models: From an art to a science
Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …
such as molecular dynamics (MD) simulations, that have gained widespread use over the …
Markov state models of biomolecular conformational dynamics
JD Chodera, F Noé - Current opinion in structural biology, 2014 - Elsevier
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 …
long-time statistical conformational dynamics of biomolecules using data from molecular …
A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories
Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function
of biomolecules since it makes nanoscale movements detectable as fluorescence signals …
of biomolecules since it makes nanoscale movements detectable as fluorescence signals …
Fluorescence resonance energy transfer at the single-molecule level
Fluorescence resonance energy transfer (FRET) is a powerful spectroscopic method for
measuring distances in the 2–8 nm range. Often, conformational changes and molecular …
measuring distances in the 2–8 nm range. Often, conformational changes and molecular …
[HTML][HTML] Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems
Highlights•Hybrid-FRET on rails automates FRET-based integrative structural
modeling.•Automated experiment design assures highest structural quality with minimal …
modeling.•Automated experiment design assures highest structural quality with minimal …
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices
Single-molecule FRET (smFRET) has become a mainstream technique for studying
biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by …
biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by …
Translation initiation is controlled by RNA folding kinetics via a ribosome drafting mechanism
A Espah Borujeni, HM Salis - Journal of the American Chemical …, 2016 - ACS Publications
RNA folding plays an important role in controlling protein synthesis as well as other cellular
processes. Existing models have focused on how RNA folding energetics control translation …
processes. Existing models have focused on how RNA folding energetics control translation …
Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently
Conformational changes underpin function and encode complex biomolecular mechanisms.
Gaining atomic-level detail of how such changes occur has the potential to reveal these …
Gaining atomic-level detail of how such changes occur has the potential to reveal these …
[HTML][HTML] Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines
Conformational dynamics of biomolecules are of fundamental importance for their function.
Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a …
Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a …
Unraveling the thousand word picture: an introduction to super-resolution data analysis
Super-resolution microscopy provides direct insight into fundamental biological processes
occurring at length scales smaller than light's diffraction limit. The analysis of data at such …
occurring at length scales smaller than light's diffraction limit. The analysis of data at such …