Volume 6 Supplement 1

9th German Conference on Chemoinformatics

Open Access

ChemicalToolBoX and its application on the study of the drug like and purchasable space

Journal of Cheminformatics20146(Suppl 1):P51

DOI: 10.1186/1758-2946-6-S1-P51

Published: 11 March 2014

The ever increasing amount of data and computational capabilities in the cheminformatics field has led to a scenario where efficient techniques for storage and processing in an integrated, modular, and easily accessible platform are in vital demand. Here, we present ChemicalToolBoX, a compilation of more than 30 tools integrated into a single computational chemistry and cheminformatics platform based on the Galaxy workflow management system [1, 2]. We have recently designed a workflow within the ChemicalToolBoX to generate a library of compounds containing around 70 million unique commercially available small molecules, i.e. the purchasable space [3]. Subsequently, we have used filtering rules based on structural patterns and chemical alarms to discard problematic molecules, representing a very large portion of the drug-like and purchasable space, along with other drug discovery data sets including more than 2 million fragments (Figure 1). Furthermore, we have computed several physicochemical descriptors to discover general trends applying to each subset.

Figure 1

Authors’ Affiliations

Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University


  1. [https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox]
  2. Grüning BA, et al: submitted
  3. Lucas X, et al: manuscript in preparation


© Lucas et al; licensee Chemistry Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.