Advances in the calculation of binding free energies
A de Ruiter, C Oostenbrink - Current opinion in structural biology, 2020 - Elsevier
Highlights•Binding free energy calculations are increasing used in drug design and
biotechnology.•We distinguish end-state methods, alchemical methods and pathway …
biotechnology.•We distinguish end-state methods, alchemical methods and pathway …
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 …
Ion dynamics and selectivity of Nav channels from molecular dynamics simulation
Z Sun, Z Gong, F ** 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 …
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 …
SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations
Host–guest binding is a challenging problem in computer simulation. The prediction of
binding affinities between hosts and guests is an important part of the statistical assessment …
binding affinities between hosts and guests is an important part of the statistical assessment …
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 …
SAMPL7 trimertrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations
Z Sun - Journal of Computer-Aided Molecular Design, 2021 - Springer
Host–guest binding remains a major challenge in modern computational modelling. The
newest 7th statistical assessment of the modeling of proteins and ligands (SAMPL) …
newest 7th statistical assessment of the modeling of proteins and ligands (SAMPL) …