Advances in computational methods for ligand binding kinetics
F Sohraby, A Nunes-Alves - Trends in Biochemical Sciences, 2023 - cell.com
Binding kinetic parameters can be correlated with drug efficacy, which in recent years led to
the development of various computational methods for predicting binding kinetic rates and …
the development of various computational methods for predicting binding kinetic rates and …
Predicting biomolecular binding kinetics: A review
Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics
Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …
However, such tasks have proven challenging in computational chemistry and biophysics …
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding
Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …
play an important role in cellular signaling. However, it is challenging to simulate both …
In silico modeling and scoring of PROTAC-mediated ternary complex poses
Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation
via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The …
via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The …
Molecular Docking and Dynamics Simulation Study of Hyrtios erectus Isolated Scalarane Sesterterpenes as Potential SARS-CoV-2 Dual Target Inhibitors
Simple Summary The ongoing coronavirus disease-2019 (COVID-19) pandemic shows
unprecedented challenges for the worldwide healthcare system. Despite the large clinical …
unprecedented challenges for the worldwide healthcare system. Despite the large clinical …
Recent progress in molecular simulation methods for drug binding kinetics
Highlights•Drug-target binding kinetics contribute to drug efficacy.•Many molecular dynamics
approaches to studying binding kinetics have been reported.•High quality datasets enable …
approaches to studying binding kinetics have been reported.•High quality datasets enable …
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 …
Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters
J Chen, W Wang, H Sun, W He - Mini Reviews in Medicinal …, 2024 - ingentaconnect.com
Rational predictions on binding kinetics parameters of drugs to targets play significant roles
in future drug designs. Full conformational samplings of targets are requisite for accurate …
in future drug designs. Full conformational samplings of targets are requisite for accurate …
Dissecting the allosteric fine-tuning of enzyme catalysis
XQ Yao, D Hamelberg - JACS Au, 2024 - ACS Publications
Fully understanding the mechanism of allosteric regulation in biomolecules requires
separating and examining all of the involved factors. In enzyme catalysis, allosteric effector …
separating and examining all of the involved factors. In enzyme catalysis, allosteric effector …