title: Mining collections of compounds with Screening Assistant 2.
abstract: BACKGROUND
  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 and 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        http://sa2.sourceforge.net/.
authors: Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311 B,P, 6759, rue de Chartres, 45067 Orléans Cedex 2, France. vchem@users.sourceforge.net.
authors: Vincent Le
authors: VL
authors: Guilloux
authors: Alban
authors: A
authors: Arrault
authors: Lionel
authors: L
authors: Colliandre
authors: Stéphane
authors: S
authors: Bourg
authors: Philippe
authors: P
authors: Vayer
authors: Luc
authors: L
authors: Morin-Allory