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

Introduction: 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.

Areas covered: 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.

Expert opinion: 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.