Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis
C Wang, PH Nguyen, K Pham, D Huynh… - Journal of …, 2016 - Wiley Online Library
Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) methods have become
widely adopted in estimating protein–ligand binding affinities due to their efficiency and high …
widely adopted in estimating protein–ligand binding affinities due to their efficiency and high …
g_mmpbsaA GROMACS Tool for High-Throughput MM-PBSA Calculations
Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), a method to estimate
interaction free energies, has been increasingly used in the study of biomolecular …
interaction free energies, has been increasingly used in the study of biomolecular …
Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?
C Mulakala, VN Viswanadhan - Journal of Molecular Graphics and …, 2013 - Elsevier
Implicit solvation methods such as MM-GBSA, when applied to evaluating protein/ligand
binding free energies, are widely believed to be accurate only for the estimation of relative …
binding free energies, are widely believed to be accurate only for the estimation of relative …
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
The Molecular Mechanics/Poisson− Boltzmann Surface Area (MM/PBSA) and the Molecular
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
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 …
Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA
G Rastelli, AD Rio, G Degliesposti… - Journal of …, 2010 - Wiley Online Library
In the drug discovery process, accurate methods of computing the affinity of small molecules
with a biological target are strongly needed. This is particularly true for molecular docking …
with a biological target are strongly needed. This is particularly true for molecular docking …
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The …
In molecular docking, it is challenging to develop a scoring function that is accurate to
conduct high‐throughput screenings. Most scoring functions implemented in popular …
conduct high‐throughput screenings. Most scoring functions implemented in popular …
Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein–protein interactions
Enhanced sampling has been extensively used to capture the conformational transitions in
protein folding, but it attracts much less attention in the studies of protein–protein …
protein folding, but it attracts much less attention in the studies of protein–protein …
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 …
Calculation of protein-ligand binding affinities
Accurate methods of computing the affinity of a small molecule with a protein are needed to
speed the discovery of new medications and biological probes. This paper reviews physics …
speed the discovery of new medications and biological probes. This paper reviews physics …