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 …
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces
We describe a general approach to designing two-dimensional (2D) protein arrays mediated
by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the …
by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the …
[HTML][HTML] Variational cross-validation of slow dynamical modes in molecular kinetics
Markov state models are a widely used method for approximating the eigenspectrum of the
molecular dynamics propagator, yielding insight into the long-timescale statistical kinetics …
molecular dynamics propagator, yielding insight into the long-timescale statistical kinetics …
Modeling molecular kinetics with tICA and the kernel trick
The allure of a molecular dynamics simulation is that, given a sufficiently accurate force field,
it can provide an atomic-level view of many interesting phenomena in biology. However, the …
it can provide an atomic-level view of many interesting phenomena in biology. However, the …
The theory of ultra-coarse-graining. 1. General principles
Coarse-grained (CG) models provide a computationally efficient means to study
biomolecular and other soft matter processes involving large numbers of atoms correlated …
biomolecular and other soft matter processes involving large numbers of atoms correlated …
[HTML][HTML] CONAN: a tool to decode dynamical information from molecular interaction maps
The analysis of contacts is a powerful tool to understand biomolecular function in a series of
contexts, from the investigation of dynamical behavior at equilibrium to the study of …
contexts, from the investigation of dynamical behavior at equilibrium to the study of …
Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules
Limited bonding valence, usually accompanied by well-defined directional interactions and
selective bonding mechanisms, is nowadays considered among the key ingredients to …
selective bonding mechanisms, is nowadays considered among the key ingredients to …
[HTML][HTML] Perspective: Markov models for long-timescale biomolecular dynamics
Molecular dynamics simulations have the potential to provide atomic-level detail and insight
to important questions in chemical physics that cannot be observed in typical experiments …
to important questions in chemical physics that cannot be observed in typical experiments …
Free energy landscape of activation in a signalling protein at atomic resolution
The interconversion between inactive and active protein states, traditionally described by
two static structures, is at the heart of signalling. However, how folded states interconvert is …
two static structures, is at the heart of signalling. However, how folded states interconvert is …