Molecular docking programs are widely used modeling tools for predicting ligand binding
modes and structure based virtual screening. In this study, six molecular docking programs …

The estimation of free energy of binding is a key problem in structure-based design. We
developed the scoring function HYDE based on a consistent description of HYdrogen bond …

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 …

Refined nearest neighbor analysis was recently introduced for the analysis of virtual
screening benchmark data sets. It constitutes a technique from the field of spatial statistics …

Benchmarks for molecular docking have historically focused on re-docking the cognate
ligand of a well-determined protein–ligand complex to measure geometric pose prediction …

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 …

Docking scoring functions are notoriously weak predictors of binding affinity. They typically
assign a common set of weights to the individual energy terms that contribute to the overall …

We developed a new empirical scoring function, HYDE, for the evaluation of protein–ligand
complexes. HYDE estimates binding free energy based on two terms for dehydration and …

The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic
structures of a collection of small molecule ligands that have been shown to bind nucleic …

An innovative molecular docking algorithm and three specialized high accuracy scoring
functions are introduced in the Lead Finder docking software. Lead Finder's algorithm for …