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 …

A new assessment criterion for docking poses is proposed in which experimental electron
density is taken into account when evaluating the ability of docking programs to reproduce …

Eleven popular scoring functions have been tested on 100 protein− ligand complexes to
evaluate their abilities to reproduce experimentally determined structures and binding …

Increased interest in covalent drug discovery led to the development of computer programs
predicting binding mode and affinity of covalent inhibitors. Here we compare the …

Automated docking is one of the most important tools for structure‐based drug design that
allows prediction of ligand binding poses and also provides an estimate of how well small …

Several different functions have been put forward for evaluating the energetics of ligand
binding to proteins. Those employed in the DOCK, GOLD and FlexX docking programs have …

Docking functions are believed to be the essential component of docking algorithms. Both
physically and statistically based functions have been proposed, but there is no consensus …

We report on the development and validation of a new version of DOCK. The algorithm has
been rewritten in a modular format, which allows for easy implementation of new scoring …

As one of the most popular computational approaches in modern structure-based drug
design, molecular docking can be used not only to identify the correct conformation of a …

We evaluated the docking accuracy of ArgusLab, which is a freely available software
program for computational docking, using experimentally determined protein–ligand …