Overview of the SAMPL6 host–guest binding affinity prediction challenge
Accurately predicting the binding affinities of small organic molecules to biological
macromolecules can greatly accelerate drug discovery by reducing the number of …
macromolecules can greatly accelerate drug discovery by reducing the number of …
On calculating free energy differences using ensembles of transition paths
The free energy of a process is the fundamental quantity that determines its spontaneity or
propensity at a given temperature. In particular, the binding free energy of a drug candidate …
propensity at a given temperature. In particular, the binding free energy of a drug candidate …
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 of Host–Guest Systems with SMIRNOFF99Frosst 1.0. 5 from the open force field initiative
Designing ligands that bind their target biomolecules with high affinity and specificity is a key
step in small-molecule drug discovery, but accurately predicting protein–ligand binding free …
step in small-molecule drug discovery, but accurately predicting protein–ligand binding free …
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 …
Accurate receptor-ligand binding free energies from fast qm conformational chemical space sampling
E Boz, M Stein - International journal of molecular sciences, 2021 - mdpi.com
Small molecule receptor-binding is dominated by weak, non-covalent interactions such as
van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand …
van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand …
Machine learning and enhanced sampling simulations for computing the potential of mean force and standard binding free energy
Computational capabilities are rapidly increasing, primarily because of the availability of
GPU-based architectures. This creates unprecedented simulative possibilities for the …
GPU-based architectures. This creates unprecedented simulative possibilities for 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) …
SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules
The physicochemical properties of a drug molecule determine the therapeutic effectiveness
of the drug. Thus, the development of fast and accurate theoretical approaches for the …
of the drug. Thus, the development of fast and accurate theoretical approaches for the …
SAMPL7: Host–guest binding prediction by molecular dynamics and quantum mechanics
Abstract Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges
provide routes to compare chemical quantities determined using computational chemistry …
provide routes to compare chemical quantities determined using computational chemistry …