Six docking programs (FlexX, GOLD, ICM, LigandFit, the Northwestern University version of
DOCK, and QXP) were evaluated in terms of their ability to reproduce experimentally …

Introduction The discovery of a new drug is a costly and lengthy endeavour. The
computational prediction of which small molecules can bind to a protein target can …

Abstract The Drug Design Data Resource (D3R) aims to identify best practice methods for
computer aided drug design through blinded ligand pose prediction and affinity challenges …

DoMCoSAR is a novel approach for statistically determining the do cking m ode that is co
nsistent with as tructure− a ctivity r elationship. The approach establishes the binding mode …

Our comparative assessment of scoring functions (CASF) benchmark is created to provide
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …

Scoring functions are often applied in combination with molecular docking methods to
predict ligand binding poses and ligand binding affinities or to identify active compounds …

Background In drug design, an efficient structure-based optimization of a ligand needs the
precise knowledge of the protein–ligand interactions. In the absence of experimental …

The ranking of ligand docking poses according to certain scoring systems to identify the best
fit is the most important step in virtual database screening for drug discovery. By focusing on …

In our previous report, we investigated the impact of protein flexibility and the presence of
water molecules on the pose-prediction accuracy of major docking programs. To complete …

A handful of molecular docking tools have been extended to enable a covalent docking.
However, all of them face the challenge brought by the covalent bond between proteins and …