The molecular basis for cellular function of intrinsically disordered protein regions
Intrinsically disordered protein regions exist in a collection of dynamic interconverting
conformations that lack a stable 3D structure. These regions are structurally heterogeneous …
conformations that lack a stable 3D structure. These regions are structurally heterogeneous …
Amyloid oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's disease, type II diabetes, and amyotrophic lateral sclerosis
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting
either the central nervous system or a variety of peripheral tissues. Structural and dynamic …
either the central nervous system or a variety of peripheral tissues. Structural and dynamic …
OPLS4: Improving force field accuracy on challenging regimes of chemical space
We report on the development and validation of the OPLS4 force field. OPLS4 builds upon
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
The all-atom additive CHARMM36 protein force field is widely used in molecular modeling
and simulations. We present its refinement, CHARMM36m (http://mackerell. umaryland …
and simulations. We present its refinement, CHARMM36m (http://mackerell. umaryland …
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity
The papain-like protease PLpro is an essential coronavirus enzyme that is required for
processing viral polyproteins to generate a functional replicase complex and enable viral …
processing viral polyproteins to generate a functional replicase complex and enable viral …
ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
Develo** a molecular dynamics force field for both folded and disordered protein states
Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural
dynamics of folded proteins and should be similarly applicable to disordered proteins and …
dynamics of folded proteins and should be similarly applicable to disordered proteins and …
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 …
Implicit solvation methods for catalysis at electrified interfaces
Implicit solvation is an effective, highly coarse-grained approach in atomic-scale simulations
to account for a surrounding liquid electrolyte on the level of a continuous polarizable …
to account for a surrounding liquid electrolyte on the level of a continuous polarizable …
Systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations
SP Kadaoluwa Pathirannahalage… - Journal of Chemical …, 2021 - ACS Publications
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …