Unsupervised learning methods for molecular simulation data
Unsupervised learning is becoming an essential tool to analyze the increasingly large
amounts of data produced by atomistic and molecular simulations, in material science, solid …
amounts of data produced by atomistic and molecular simulations, in material science, solid …
Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer
BACKGROUND Biomolecular mechanisms are typically inferred from static structural
“snapshots” obtained by x-ray crystallography, nuclear magnetic resonance (NMR) …
“snapshots” obtained by x-ray crystallography, nuclear magnetic resonance (NMR) …
Hierarchical materials from high information content macromolecular building blocks: construction, dynamic interventions, and prediction
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature.
Because hierarchy gives rise to unique properties and functions, many have sought …
Because hierarchy gives rise to unique properties and functions, many have sought …
Water dispersion interactions strongly influence simulated structural properties of disordered protein states
Many proteins can be partially or completely disordered under physiological conditions.
Structural characterization of these disordered states using experimental methods can be …
Structural characterization of these disordered states using experimental methods can be …
Markov state models of biomolecular conformational dynamics
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 …
Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
Improvements in Markov state model construction reveal many non-native interactions in the folding of NTL9
Markov State Models (MSMs) provide an automated framework to investigate the dynamical
properties of high-dimensional molecular simulations. These models can provide a human …
properties of high-dimensional molecular simulations. These models can provide a human …
[HTML][HTML] Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
Highlights•The accuracy of physical models used in protein-folding simulations is
assessed.•This assessment is based on data from very long molecular dynamics …
assessed.•This assessment is based on data from very long molecular dynamics …
To milliseconds and beyond: challenges in the simulation of protein folding
Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding
have long been considered a holy grail of computational biology. Due to the large system …
have long been considered a holy grail of computational biology. Due to the large system …
Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water
A substantial fraction of the proteome is intrinsically disordered, and even well-folded
proteins adopt non-native geometries during synthesis, folding, transport, and turnover …
proteins adopt non-native geometries during synthesis, folding, transport, and turnover …