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Continuum molecular electrostatics, salt effects, and counterion binding—A review of the Poisson–Boltzmann theory and its modifications
TLDR
This work is a review of the Poisson–Boltzmann (PB) continuum electrostatics theory and its modifications, with a focus on salt effects and counterion binding, and discusses the conventional PB equation, the corresponding functionals of the electrostatic free energy, including a connection to DFT. Expand
Binding Pathways of Ligands to HIV‐1 Protease: Coarse‐grained and Atomistic Simulations
TLDR
This is the first molecular dynamics simulation of modeling the association of a ligand with the protease and it is found that a protease substrate successfully binds to the protein when the flaps are fully open. Expand
Secondary structures of native and pathogenic huntingtin N-terminal fragments.
TLDR
It is found that corresponding regions in both fragments fold to similar secondary structures; the headpiece and polyQ stretch adopt mainly α-helical conformations, and polyP(11) forms the PP II-type helix. Expand
Brownian dynamics simulations on CPU and GPU with BD_BOX
TLDR
A software package, BD_BOX, for multiscale Brownian dynamics simulations, which can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse‐grained bead models. Expand
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.
TLDR
Brownian dynamics simulations in a coarse-grained model are applied to study the gated association rate constants of HIV-1 proteases and drugs and suggest that the flap flexibility and the opening frequency of the wild-type, the G48V and L90M mutants are similar, but the flaps of the variant open less frequently, resulting in a lower gated rate constant. Expand
Thermodynamic linkage between the binding of protons and inhibitors to HIV‐1 protease
TLDR
Computations and measurements related to changes in protonation and to the thermodynamic linkage between protonated and inhibition are presented and implications for the accurate calculation of pKas in complex protein environments are presented. Expand
Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study.
TLDR
The results suggest that the H3 tail may stabilize the nucleosome in the open state during the initial stages of theucleosome remodeling process, and the physical consistency of the CG long-lived open state was verified. Expand
Flap opening dynamics in HIV-1 protease explored with a coarse-grained model.
TLDR
A one-bead coarse-grained model that enables dynamical simulations of proteins on the time scale of tens of microseconds is presented and is found to be reliable for application to substrate docking simulations, which are currently in progress. Expand
Exploring global motions and correlations in the ribosome.
TLDR
A low-resolution anharmonic network model that allows for the evolution of tertiary structure and long-scale sampling was developed and parameterized finds that functionally important movements of L7/L12 and L1 lateral stalks are anticorrelated. Expand
HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics.
TLDR
Analysis of the encounter of a peptide substrate with the native HIV-1 protease, the mechanism of substrate incorporation in the binding cleft, and the dissociation of products after substrate hydrolysis suggests some mechanistic principles for how the flexibility of the protein may be involved in ligand binding and release. Expand
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