Molecular docking is a computational method for predicting the placement of ligands in the
binding sites of their receptor (s). In this review, we discuss the methodological …

Binding MOAD is a database of protein–ligand complexes and their affinities with many
structured relationships across the dataset. The project has been in development for over 20 …

Prediction of the bound configuration of small-molecule ligands that differ substantially from
the cognate ligand of a protein co-crystal structure is much more challenging than re …

Binding of anions using macrocyclic structures with a nonpolar interior using the CH··· anion
interaction as the recognition motif has gained popularity in the past few years, and such …

A pharmacophore represents a simple and intuitive concept that have been used for
decades in medicinal chemistry. The use of three-dimensional chemical feature ensembles …

We introduce the QuanSA method for inducing physically meaningful field-based models of
ligand binding pockets based on structure-activity data alone. The method is closely related …

The structural resolution of a bound ligand–receptor complex is a key asset to efficiently
drive lead optimization in drug design. However, structural resolution of many drug targets …

Surflex-QMOD integrates chemical structure and activity data to produce physically-realistic
models for binding affinity prediction. Here, we apply QMOD to a 3D-QSAR benchmark …