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 …
Recent developments and applications of the MMPBSA method
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been
widely applied as an efficient and reliable free energy simulation method to model molecular …
widely applied as an efficient and reliable free energy simulation method to model molecular …
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 …
Avoiding false positive conclusions in molecular simulation: the importance of replicas
Molecular simulations are a computational technique used to investigate the dynamics of
proteins and other molecules. The free energy landscape of these simulations is often …
proteins and other molecules. The free energy landscape of these simulations is often …
Accurate calculation of the absolute free energy of binding for drug molecules
Accurate prediction of binding affinities has been a central goal of computational chemistry
for decades, yet remains elusive. Despite good progress, the required accuracy for use in a …
for decades, yet remains elusive. Despite good progress, the required accuracy for use in a …
Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …
Thermodynamics and kinetics of drug-target binding by molecular simulation
S Decherchi, A Cavalli - Chemical Reviews, 2020 - ACS Publications
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
Screening of potential inhibitors targeting the main protease structure of SARS-CoV-2 via molecular docking, and approach with molecular dynamics, RMSD, RMSF, H …
AM da Fonseca, BJ Caluaco, JMC Madureira… - Molecular …, 2023 - Springer
Abstract Severe Acute Respiratory Syndrome caused by a coronavirus is a recent viral
infection. There is no scientific evidence or clinical trials to indicate that possible therapies …
infection. There is no scientific evidence or clinical trials to indicate that possible therapies …
Rapid, accurate, precise, and reliable relative free energy prediction using ensemble based thermodynamic integration
The accurate prediction of the binding affinities of ligands to proteins is a major goal in drug
discovery and personalized medicine. The time taken to make such predictions is of similar …
discovery and personalized medicine. The time taken to make such predictions is of similar …
Statistical analysis on the performance of molecular mechanics poisson–boltzmann surface area versus absolute binding free energy calculations: Bromodomains as …
Binding free energy calculations that make use of alchemical pathways are becoming
increasingly feasible thanks to advances in hardware and algorithms. Although relative …
increasingly feasible thanks to advances in hardware and algorithms. Although relative …