Electrostatic interactions in protein structure, folding, binding, and condensation
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …
specific electrostatic interactions, impart important properties to proteins. Modulation of the …
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 …
Improvements to the APBS biomolecular solvation software suite
Abstract The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages that have …
the equations of continuum electrostatics for large biomolecular assemblages that have …
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 …
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
BR Miller III, TD McGee Jr, JM Swails… - Journal of chemical …, 2012 - ACS Publications
MM-PBSA is a post-processing end-state method to calculate free energies of molecules in
solution. MMPBSA. py is a program written in Python for streamlining end-state free energy …
solution. MMPBSA. py is a program written in Python for streamlining end-state free energy …
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 …
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. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA …
With the rapid development of computational techniques and hardware, more rigorous and
precise theoretical models have been used to predict the binding affinities of a large number …
precise theoretical models have been used to predict the binding affinities of a large number …
[PDF][PDF] Amber 10
Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …
dynamics simulations, particularly on biomolecules. None of the individual programs carries …