Molecular dynamics simulations in drug discovery and pharmaceutical development
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …
development process. In this review, we give a broad overview of the current application …
Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy
The last 15 years have seen a paradigm shift in our understanding of protein biochemistry,
with the realization that an unexpectedly high fraction of the human genome codes for …
with the realization that an unexpectedly high fraction of the human genome codes for …
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 …
Molecular interactions contributing to FUS SYGQ LC-RGG phase separation and co-partitioning with RNA polymerase II heptads
The RNA-binding protein FUS (Fused in Sarcoma) mediates phase separation in
biomolecular condensates and functions in transcription by clustering with RNA polymerase …
biomolecular condensates and functions in transcription by clustering with RNA polymerase …
Structural ensembles of intrinsically disordered proteins depend strongly on force field: a comparison to experiment
Intrinsically disordered proteins (IDPs) are notoriously challenging to study both
experimentally and computationally. The structure of IDPs cannot be described by a single …
experimentally and computationally. The structure of IDPs cannot be described by a single …
Building a more predictive protein force field: a systematic and reproducible route to AMBER-FB15
The increasing availability of high-quality experimental data and first-principles calculations
creates opportunities for develo** more accurate empirical force fields for simulation of …
creates opportunities for develo** more accurate empirical force fields for simulation of …
Systematic improvement of a classical molecular model of water
We report the iAMOEBA (“inexpensive AMOEBA”) classical polarizable water model. The
iAMOEBA model uses a direct approximation to describe electronic polarizability, in which …
iAMOEBA model uses a direct approximation to describe electronic polarizability, in which …
Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil
The pathogenesis of Alzheimer's disease is characterized by the aggregation and fibrillation
of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid plaques. Despite strong potential …
of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid plaques. Despite strong potential …
Constructing ensembles for intrinsically disordered proteins
The relatively flat energy landscapes associated with intrinsically disordered proteins makes
modeling these systems especially problematic. A comprehensive model for these proteins …
modeling these systems especially problematic. A comprehensive model for these proteins …
Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape
Amyloids can have normal biological functions. 1r3 However, amyloidogenic proteins can
also form unwanted oligomeric or polymeric aggregates when disturbed from their native …
also form unwanted oligomeric or polymeric aggregates when disturbed from their native …