Mining Chemical Libraries with “Screening Assistant 2” by Vincent Le Guilloux, Alban Arrault, Lionel Colliandre, Stéphane Bourg, Philippe Vayer and Luc Morin-Allory (Journal of Cheminformatics 2012, 4:20 doi:10.1186/1758-2946-4-20)
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 in nite 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, sca old 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/.
And you thought you had “big data:”
Exploring biology through the activity of small molecules is an established paradigm used in drug research for several decades now [1, 2]. Today, a state of the art drug discovery program often begins with screening campaigns aiming at the identification of novel biologically active molecules. In the recent years, the rise of High Throughput Screening (HTS), combinatorial chemistry and the availability of large compound collections has led to a dramatic increase in the size of screening libraries, for both private companies and public organisations [3, 4]. Yet, despite these constantly increasing capabilities, various authors have stressed the need to design better instead of larger screening libraries [5–9]. Chemical space is indeed known to be almost infinite, and selecting the appropriate regions to explore for the problem at hand remains a challenging task. (emphasis added)
I would paraphrase the highlighted part to read:
Semantic space is known to be infinite, and selecting appropriate regions for the problem at hand remains a challenging task.
Or to put it differently, if I have a mapping strategy that works for clinical information systems or (U.S.) DoD contracting records or some other domain, that’s great!
I don’t need to look for a universal mapping solution.
Not to mention that I can produce results (and get paid) more quickly than waiting for a universal mapping solution.