A general picture of cucurbit [8] uril host–guest binding
Describing, understanding, and designing complex interaction networks within
macromolecular systems remain challenging in modern chemical research. Host–guest …
macromolecular systems remain challenging in modern chemical research. Host–guest …
Conformational transformation of switch domains in GDP/K-Ras induced by G13 mutants: An investigation through Gaussian accelerated molecular dynamics …
J Chen, L Wang, W Wang, H Sun, L Pang… - Computers in Biology and …, 2021 - Elsevier
Mutations in K-Ras are involved in a large number of all human cancers, thus, K-Ras is
regarded as a promising target for anticancer drug design. Understanding the target roles of …
regarded as a promising target for anticancer drug design. Understanding the target roles of …
Binding of inhibitors to BACE1 affected by pH-dependent protonation: An exploration from multiple replica Gaussian accelerated molecular dynamics and MM-GBSA …
J Chen, S Zhang, W Wang, H Sun… - ACS Chemical …, 2021 - ACS Publications
To date, inhibiting the activity of β-amyloid cleaving enzyme 1 (BACE1) has been
considered an efficient approach for treating Alzheimer's disease (AD). In the current work …
considered an efficient approach for treating Alzheimer's disease (AD). In the current work …
Primary vs secondary: Directionalized guest coordination in β-cyclodextrin derivatives
Z Sun, L Zheng, K Wang, Z Huai, Z Liu - Carbohydrate Polymers, 2022 - Elsevier
In computational modelling of cyclodextrin (CD) host-guest binding, often only a single
binding mode is considered. However, due to the asymmetric feature of CD, the guest can …
binding mode is considered. However, due to the asymmetric feature of CD, the guest can …
Ion dynamics and selectivity of Nav channels from molecular dynamics simulation
The voltage-gated sodium (Na v) channels are crucial in initiating and propagating action
potentials in excitable cells. In this work, with atomistic molecular simulations employing …
potentials in excitable cells. In this work, with atomistic molecular simulations employing …
Conformational fluctuations in GTP-bound K-Ras: A metadynamics perspective with harmonic linear discriminant analysis
X Wang - Journal of Chemical Information and Modeling, 2021 - ACS Publications
Biomacromolecules often undergo significant conformational rearrangements during
function. In proteins, these motions typically consist in nontrivial, concerted rearrangement of …
function. In proteins, these motions typically consist in nontrivial, concerted rearrangement of …
SAMPL7 TrimerTrip host–guest binding affinities from extensive alchemical and end-point free energy calculations
Z Huai, H Yang, X Li, Z Sun - Journal of Computer-Aided Molecular …, 2021 - Springer
The prediction of host–guest binding affinities with computational modelling is still a
challenging task. In the 7th statistical assessment of the modeling of proteins and ligands …
challenging task. In the 7th statistical assessment of the modeling of proteins and ligands …
Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics
J Chen, W Wang, H Sun, L Pang, B Yin - Journal of Computer-Aided …, 2020 - Springer
Anaplastic lymphoma kinase (ALK) has been thought to be a prospective target of anti-drug
resistance design in treatment of tumors and specific neuron diseases. It is highly useful for …
resistance design in treatment of tumors and specific neuron diseases. It is highly useful for …
Binding thermodynamics and interaction patterns of inhibitor-major urinary protein-I binding from extensive free-energy calculations: benchmarking AMBER force …
Mouse major urinary protein (MUP) plays a key role in the pheromone communication
system. The one-end-closed β-barrel of MUP-I forms a small, deep, and hydrophobic central …
system. The one-end-closed β-barrel of MUP-I forms a small, deep, and hydrophobic central …
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host–Guest Systems
End-point free-energy methods as an indispensable component in virtual screening are
commonly recognized as a tool with a certain level of screening power in pharmaceutical …
commonly recognized as a tool with a certain level of screening power in pharmaceutical …