Predicting binding free energies: frontiers and benchmarks
Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …
for biomolecular complexes. These calculations begin with a detailed description of a …
Thermodynamics and kinetics of drug-target binding by molecular simulation
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field
We introduce the Open Force Field (OpenFF) 2.0. 0 small molecule force field for drug-like
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
Role of molecular dynamics and related methods in drug discovery
Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …
Free energy methods in drug design: prospects of “alchemical perturbation” in medicinal chemistry: miniperspective
BJ Williams-Noonan, E Yuriev… - Journal of medicinal …, 2018 - ACS Publications
Underpinning all drug discovery projects is the interaction between a drug and its target,
usually a protein. Thus, improved methods for predicting the magnitude of protein–ligand …
usually a protein. Thus, improved methods for predicting the magnitude of protein–ligand …
Biomolecular force field parameterization via atoms-in-molecule electron density partitioning
Molecular mechanics force fields, which are commonly used in biomolecular modeling and
computer-aided drug design, typically treat nonbonded interactions using a limited library of …
computer-aided drug design, typically treat nonbonded interactions using a limited library of …
Transferable machine learning interatomic potential for bond dissociation energy prediction of drug-like molecules
We present a transferable MACE interatomic potential that is applicable to open-and closed-
shell drug-like molecules containing hydrogen, carbon, and oxygen atoms. Including an …
shell drug-like molecules containing hydrogen, carbon, and oxygen atoms. Including an …
Current tools and methods in molecular dynamics (MD) simulations for drug design
M Hernández-Rodríguez… - Current medicinal …, 2016 - benthamdirect.com
Molecular Dynamics (MD) simulations is a computational method that employs Newton's
laws to evaluate the motions of water, ions, small molecules, and macromolecules or more …
laws to evaluate the motions of water, ions, small molecules, and macromolecules or more …
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 …
Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method
A new methodology termed Single Amino Acid Mutation based change in Binding free
Energy (SAAMBE) was developed to predict the changes of the binding free energy caused …
Energy (SAAMBE) was developed to predict the changes of the binding free energy caused …