End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectives
Food-derived bioactive peptides (FBPs) are gaining interest due to their great potential in
agricultural byproduct valorization and high-activity peptide screening. The introduction of …
agricultural byproduct valorization and high-activity peptide screening. The introduction of …
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
S Genheden, U Ryde - Expert opinion on drug discovery, 2015 - Taylor & Francis
Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …
Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
Entropy effects play an important role in drug–target interactions, but the entropic
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols …
By using different evaluation strategies, we systemically evaluated the performance of
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models
Here, we systematically investigated how the force fields and the partial charge models for
ligands affect the ranking performance of the binding free energies predicted by the …
ligands affect the ranking performance of the binding free energies predicted by the …
An effective MM/GBSA protocol for absolute binding free energy calculations: A case study on SARS-CoV-2 spike protein and the human ACE2 receptor
N Forouzesh, N Mishra - Molecules, 2021 - mdpi.com
The binding free energy calculation of protein–ligand complexes is necessary for research
into virus–host interactions and the relevant applications in drug discovery. However, many …
into virus–host interactions and the relevant applications in drug discovery. However, many …
Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM
Staphylococcus aureus is resistant to β-lactam antibiotics and causes several skin diseases
to life-threatening diseases. FmtA is found to be one of the main factors involved in …
to life-threatening diseases. FmtA is found to be one of the main factors involved in …
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 …
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus
FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural
folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking …
folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking …