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 …
[HTML][HTML] Molecular modelling of ionic liquids: General guidelines on fixed-charge force fields for balanced descriptions
It has been increasingly common to investigate dynamic and thermodynamic properties of
green solvents at atomistic scales with molecular simulation. In this work, we present a …
green solvents at atomistic scales with molecular simulation. In this work, we present a …
Thermodynamic insights of base flip** in TNA duplex: force fields, salt concentrations, and free-energy simulation methods
Threofuranosyl nucleic acid (TNA) is an analogue of DNA with a shift in the internucleotide
linkages from the wild-type 5'-to-3'direction to 3'-to-2.'This alteration leads to higher chemical …
linkages from the wild-type 5'-to-3'direction to 3'-to-2.'This alteration leads to higher chemical …
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 …
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 …
Seeding the multi-dimensional nonequilibrium pulling for Hamiltonian variation: indirect nonequilibrium free energy simulations at QM levels
The combination of free energy simulations in the alchemical and configurational spaces
provides a feasible route to access the thermodynamic profiles under a computationally …
provides a feasible route to access the thermodynamic profiles under a computationally …
Distributions of bubble lifetimes and bubble lengths in DNA
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at
physiological temperature, by performing extensive molecular dynamics simulations with the …
physiological temperature, by performing extensive molecular dynamics simulations with the …
BAR‐Based Multi‐Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region
Z Sun, Z Liu - Advanced Theory and Simulations, 2021 - Wiley Online Library
The indirect free energy simulation at quantum mechanics (QM)/molecular mechanics (MM)
levels provides a feasible alternative to direct QM/MM simulations. The main idea under the …
levels provides a feasible alternative to direct QM/MM simulations. The main idea under the …
Sulfur-substitution-induced base flip** in the DNA duplex
Base flip** is widely observed in a number of important biological processes. The genetic
codes deposited inside the DNA duplex become accessible to external agents upon base …
codes deposited inside the DNA duplex become accessible to external agents upon base …
BAR-based multi-dimensional nonequilibrium pulling for indirect construction of a QM/MM free energy landscape
Construction of free energy landscapes at the quantum mechanics (QM) level is
computationally demanding. As shown in previous studies, by employing an indirect scheme …
computationally demanding. As shown in previous studies, by employing an indirect scheme …