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 …
[HTML][HTML] 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 …
Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study
J Wang - Journal of chemical information and modeling, 2020 - ACS Publications
The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes
possible treatment strategies using drugs on the market. It is very efficient to apply computer …
possible treatment strategies using drugs on the market. It is very efficient to apply computer …
Decoding the identification mechanism of an SAM-III Riboswitch on ligands through multiple independent Gaussian-accelerated molecular dynamics simulations
J Chen, Q Zeng, W Wang, H Sun… - Journal of Chemical …, 2022 - ACS Publications
S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation
of bacterial gene expression at the level of transcription attenuation or translation inhibition …
of bacterial gene expression at the level of transcription attenuation or translation inhibition …
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 …
Dielectric continuum methods for quantum chemistry
JM Herbert - Wiley Interdisciplinary Reviews: Computational …, 2021 - Wiley Online Library
This review describes the theory and implementation of implicit solvation models based on
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
Improved protein–ligand binding affinity prediction with structure-based deep fusion inference
Predicting accurate protein–ligand binding affinities is an important task in drug discovery
but remains a challenge even with computationally expensive biophysics-based energy …
but remains a challenge even with computationally expensive biophysics-based energy …
Structure-based drug repurposing: Traditional and advanced AI/ML-aided methods
Highlights•Repurposing existing drugs for new diseases is cost effective and time saving.•In
silico methods are crucial for rapid drug screening in the early stages.•Machine learning …
silico methods are crucial for rapid drug screening in the early stages.•Machine learning …
Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses …
Understanding protein–protein interactions (PPIs) is quite important to elucidate crucial
biological processes and even design compounds that interfere with PPIs with …
biological processes and even design compounds that interfere with PPIs with …
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 …