A key metric to assess molecular docking remains ligand enrichment against challenging
decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for …

Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid
bias, decoys should resemble ligands physically, so that enrichment is not simply a …

Molecular docking is the most practical approach to leverage protein structure for ligand
discovery, but the technique retains important liabilities that make it challenging to deploy on …

Enrichment of ligands versus property-matched decoys is widely used to test and optimize
docking library screens. However, the unconstrained optimization of enrichment alone can …

We present DrugScore2018, a new version of the knowledge-based scoring function
DrugScore, which builds upon the same formalism used to derive DrugScore but exploits a …

The field of machine learning for drug discovery is witnessing an explosion of novel
methods. These methods are often benchmarked on simple physicochemical properties …

This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …

The Surflex flexible molecular docking method has been generalized and extended in two
primary areas related to the search component of docking. First, incorporation of a small …

Molecular docking remains an important tool for structure-based screening to find new
ligands and chemical probes. As docking ambitions grow to include new scoring function …

In structure-based virtual screening (SBVS), a binding site on a protein structure is used to
search for ligands with favorable nonbonded interactions. Because it is computationally …