Ligand-binding affinity estimates supported by quantum-mechanical methods
One of the largest challenges of computational chemistry is calculation of accurate free
energies for the binding of a small molecule to a biological macromolecule, which has …
energies for the binding of a small molecule to a biological macromolecule, which has …
Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery
Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
Applications of large-scale density functional theory in biology
Density functional theory (DFT) has become a routine tool for the computation of electronic
structure in the physics, materials and chemistry fields. Yet the application of traditional DFT …
structure in the physics, materials and chemistry fields. Yet the application of traditional DFT …
Development of a robust indirect approach for MM→ QM free energy calculations that combines force-matched reference potential and Bennett's acceptance ratio …
TJ Giese, DM York - Journal of chemical theory and computation, 2019 - ACS Publications
We use the PBE0/6-31G* density functional method to perform ab initio quantum
mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under …
mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under …
Calculations of solvation free energy through energy reweighting from molecular mechanics to quantum mechanics
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical
Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The …
Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The …
Accelerating QM/MM free energy computations via intramolecular force matching
The calculation of free energy differences between levels of theory has numerous potential
pitfalls. Chief among them is the lack of overlap, ie, ensembles generated at one level of …
pitfalls. Chief among them is the lack of overlap, ie, ensembles generated at one level of …
Use of nonequilibrium work methods to compute free energy differences between molecular mechanical and quantum mechanical representations of molecular …
Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians
remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on …
remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on …
[PDF][PDF] Docking and ligand binding affinity: uses and pitfalls
MJR Yunta - Am. J. Model. Optim, 2016 - researchgate.net
In this review article, we will explore the foundations of different classes of docking and
scoring functions, their possible limitations, and their suitable application domains. We also …
scoring functions, their possible limitations, and their suitable application domains. We also …
Comparison of QM/MM methods to obtain ligand-binding free energies
We have compared two approaches to calculate relative binding free energies employing
molecular dynamics simulations at the combined quantum-mechanical/molecular …
molecular dynamics simulations at the combined quantum-mechanical/molecular …
On the convergence of multi-scale free energy simulations
In this work, we employ simple model systems to evaluate the relative performance of two of
the most important free energy methods: The Zwanzig equation (also known as 'Free energy …
the most important free energy methods: The Zwanzig equation (also known as 'Free energy …