The state of the art of various computational aspects of docking-based virtual screening of
database of small molecules is presented. The review encompasses the different search …

Ligand flexibility is an important problem in molecular docking and virtual screening. To
address this challenge, we investigate a hierarchical pre-organization of multiple …

We implemented a novel approach to score water mediation and displacement in the
protein− ligand docking program GOLD. The method allows water molecules to switch on …

Motivation: Virtual screening of molecular compound libraries is a potentially powerful and
inexpensive method for the discovery of novel lead compounds for drug development. The …

Virtual screening can reduce costs and increase hit rates for lead discovery by eliminating
the need for robotics, reagent acquisition or production, and compound storage facilities …

We developed a pharmacophorebased evolutionary approach for virtual screening. This
tool, termed the Generic Evolutionary Method for molecular DOCKing (GEMDOCK) …

A protocol was devised in which FRED, DOCK, and Surflex were combined in a multistep
virtual ligand screening (VLS) procedure to screen the pocket of four different proteins. One …

CDC25 dual-specificity phosphatases are essential key regulators of eukaryotic cell cycle
progression and the CDC25A and B isoforms are over-expressed in different tumors and …

PDZ domains are important scaffolding modules that typically bind to the C-termini of their
interaction partners. Several structures of such complexes have been solved, revealing a …

Combinatorial chemistry and library design have been reconciled by applying simple
medicinal chemistry concepts to virtual library design. The herein reported “Scaffold-Linker …