… are not yet clear, though one study provides evidence that soft docking yields worse
enrichment of known ligands than does docking into multiple structures of the receptor (39). …

… for binding affinity data of these 5671 protein−ligand complexes in … Fortunately, almost every
structure deposited in PDB is … If a PDB structure is indeed a protein−ligand complex and if …

… high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD
has … Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates …

… have emerged as a useful tool in structure-based ligand design. Here we give an … ligand
binding free energies from molecular dynamics simulations. A notable feature is that the binding …

… understanding binding affinities across the entire set of ligands. Interesting outliers that bind
… If the ligand structure is only partially buried, smaller values are found. If we assume that the …

… Also, because the programs examined in this study could not consistently predict ligand
binding affinities even with X-ray complex structures, the question of whether rigid-receptor …

… ligand structures and binding affinity. The first deep neural networks (DNNs) to predict binding
affinities were convolutional neural networks (CNNs) reading a protein–ligand complex as …

… to predict the structure of the ligand–receptor complex and estimate the binding affinity
using these energy functions. The most commonly used one is to change the structure until a …

… Search capabilities include queries by target name; ligand name; affinity range; chemical
structure, substructure and similarity; and target sequence, via BLAST (14). Query results are …

… a hybrid methodology to predict the binding affinities for a highly diverse dataset of protein−ligand
complexes using concepts from both structure-based and ligand-based approaches. It …