Three-dimensional structure generators of drug-like compounds: DG-AMMOS, an open-source package

Drug discovery is a time consuming and costly process. Thus, a trend towards the use of in silico approaches such as structure- and ligand-based virtual screening methods to speed up the process has gained significant momentum in recent years. Most of these in silico applications require a good quality 3D structure of the small drug-like molecules as input.

This article reviews the algorithm and validation of the open-source software DG-AMMOS, a tool that generates the 3D conformation of small molecules using distance geometry construction and molecular mechanics optimization comparing its performance with some related free and commercial packages.

The number of chemo/bioinformatics free and/or open-source tools assisting drug discovery projects is increasing, and many successful contributions making use of these computer programs have been reported. DG-AMMOS is an efficient 3D structure generator engine that provides fast and reliable generation of 3D structures and contributes to the preparation of a compound collection. DG-AMMOS can still be improved and an increased speed and user-friendly interface in addition to the implementation of workflow engines will increase its effectiveness.