Stabilizing and modulating color by copigmentation: Insights from theory and experiment
Natural anthocyanin pigments/dyes and phenolic copigments/co-dyes form noncovalent
complexes, which stabilize and modulate (in particular blue, violet, and red) colors in …
complexes, which stabilize and modulate (in particular blue, violet, and red) colors in …
Approaches to the description and prediction of the binding affinity of small‐molecule ligands to macromolecular receptors
The influence of a xenobiotic compound on an organism is usually summarized by the
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …
generating pathways and rate constants for rare events such as protein folding and protein …
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 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 …
Interaction entropy: A new paradigm for highly efficient and reliable computation of protein–ligand binding free energy
Efficient and reliable calculation of protein–ligand binding free energy is a grand challenge
in computational biology and is of critical importance in drug design and many other …
in computational biology and is of critical importance in drug design and many other …
On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi
Implicit methods for modeling protein electrostatics require dielectric properties of the system
to be known, in particular, the value of the dielectric constant of protein. While numerous …
to be known, in particular, the value of the dielectric constant of protein. While numerous …
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 …
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 …
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 …