Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Multiscale modeling of keratin, collagen, elastin and related human diseases: Perspectives from atomistic to coarse-grained molecular dynamics simulations
Scleroproteins are an important category of proteins within the human body that adopt
filamentous, elongated conformations in contrast with typical globular proteins. These …
filamentous, elongated conformations in contrast with typical globular proteins. These …
[HTML][HTML] Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine
The functions and activities of proteins are closely related to their structures and dynamics,
and their interactions with ligands. Knowledge of the mechanistic events of proteins' …
and their interactions with ligands. Knowledge of the mechanistic events of proteins' …
Effect of atomic charge, solvation, entropy, and ligand protonation state on MM‐PB (GB) SA binding energies of HIV protease
DP Oehme, RTC Brownlee… - Journal of computational …, 2012 - Wiley Online Library
Abstract The molecular mechanics‐Poisson‐Boltzmann surface area (MM‐PBSA) and MM‐
generalized‐Born surface area (MM‐GBSA) approaches are commonly used in molecular …
generalized‐Born surface area (MM‐GBSA) approaches are commonly used in molecular …
Dynamics of a spherical self-propelled tracer in a polymeric medium: interplay of self-propulsion, stickiness, and crowding
We employ computer simulations to study the dynamics of a self-propelled spherical tracer
particle in a viscoelastic medium, made of a long polymer chain. Here, the interplay between …
particle in a viscoelastic medium, made of a long polymer chain. Here, the interplay between …
Mechanism of the association pathways for a pair of fast and slow binding ligands of HIV-1 protease
YM Huang, MAV Raymundo, W Chen, CA Chang - Biochemistry, 2017 - ACS Publications
Equilibrium constants, together with kinetic rate constants of binding, are key factors in the
efficacy and safety of drug compounds, informing drug design. However, the association …
efficacy and safety of drug compounds, informing drug design. However, the association …
Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations
The conformational dynamics in the flaps of HIV-1 protease plays a crucial role in the
mechanism of substrate binding. We develop a kinetic network model, constructed from …
mechanism of substrate binding. We develop a kinetic network model, constructed from …
Functionalized carbon nanotubes as an alternative to traditional anti-HIV-1 protease inhibitors: An understanding towards Nano-medicine development through MD …
Abstract The Human Immunodeficiency Virus (HIV) has been the source of epidemic
infection of AIDS for a longer period. One of the most difficult tasks is identifying novel …
infection of AIDS for a longer period. One of the most difficult tasks is identifying novel …
[HTML][HTML] Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket
To understand the underlying mechanisms of significant differences in dissociation rate
constant among different inhibitors for HIV-1 protease, we performed steered molecular …
constant among different inhibitors for HIV-1 protease, we performed steered molecular …
Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts
The conformational landscape of HIV-1 protease (PR) can be experimentally characterized
by pulsed-EPR double electron–electron resonance (DEER). For this characterization …
by pulsed-EPR double electron–electron resonance (DEER). For this characterization …