Molecular dynamics simulations: advances and applications
Molecular dynamics simulations have evolved into a mature technique that can be used
effectively to understand macromolecular structure-to-function relationships. Present …
effectively to understand macromolecular structure-to-function relationships. Present …
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 …
Anton 3: twenty microseconds of molecular dynamics simulation before lunch
Anton 3 is the newest member in a family of supercomputers specially designed for atomic-
level simulation of molecules relevant to biology (eg, DNA, proteins, and drug molecules) …
level simulation of molecules relevant to biology (eg, DNA, proteins, and drug molecules) …
Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer
Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics
simulations that achieves significant gains in performance, programmability, and capacity …
simulations that achieves significant gains in performance, programmability, and capacity …
Balanced protein–water interactions improve properties of disordered proteins and non-specific protein association
Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
AlphaFold2: a role for disordered protein/region prediction?
The development of AlphaFold2 marked a paradigm-shift in the structural biology
community. Herein, we assess the ability of AlphaFold2 to predict disordered regions …
community. Herein, we assess the ability of AlphaFold2 to predict disordered regions …
Native contacts determine protein folding mechanisms in atomistic simulations
The recent availability of long equilibrium simulations of protein folding in atomistic detail for
more than 10 proteins allows us to identify the key interactions driving folding. We find that …
more than 10 proteins allows us to identify the key interactions driving folding. We find that …
Machine learning coarse-grained potentials of protein thermodynamics
A generalized understanding of protein dynamics is an unsolved scientific problem, the
solution of which is critical to the interpretation of the structure-function relationships that …
solution of which is critical to the interpretation of the structure-function relationships that …
[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 …
Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs)
It has long been axiomatic that a protein's structure determines its function. Intrinsically
disordered proteins (IDPs) and disordered protein regions (IDRs) defy this structure …
disordered proteins (IDPs) and disordered protein regions (IDRs) defy this structure …