Mining collections of compounds with Screening Assistant 2

Vincent Guilloux, Alban Arrault, Lionel Colliandre, Stéphane Bourg, Philippe Vayer, Luc Morin-Allory
2012 Journal of Cheminformatics  
High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. Results: We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage
more » ... d analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Conclusions: Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at
doi:10.1186/1758-2946-4-20 pmid:23327565 pmcid:PMC3547782 fatcat:y5twr7xhsbeihhjb4uh6l7phvm