Conspectus In structure-based drug design, scoring functions are widely used for fast
evaluation of protein–ligand interactions. They are often applied in combination with …

The ability to computationally predict protein-small molecule binding affinities with high
accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial …

Although deep learning approaches have had tremendous success in image, video and
audio processing, computer vision, and speech recognition, their applications to three …

Scoring functions are a class of computational methods widely applied in structure-based
drug design for evaluating protein–ligand interactions. Dozens of scoring functions have …

Approaches for computing small molecule binding free energies based on molecular
simulations are now regularly being employed by academic and industry practitioners to …

Accurately predicting the binding affinities of small organic molecules to biological
macromolecules can greatly accelerate drug discovery by reducing the number of …

Designing ligands that bind their target biomolecules with high affinity and specificity is a key
step in small-molecule drug discovery, but accurately predicting protein–ligand binding free …

Fast and accurate biomolecular free energy estimation has been a significant interest for
decades, and with recent advances in computer hardware, interest in new method …

Conventional protein: ligand crystallographic refinement uses stereochemistry restraints
coupled with a rudimentary energy functional to ensure the correct geometry of the model of …

We present a feature functional theory–binding predictor (FFT–BP) for the protein–ligand
binding affinity prediction. The underpinning assumptions of FFT–BP are as follows:(1) …