Screening Assistant 2 v1.0 RC1

Documentation index

Last edited: 18/11/2011
Sourceforge: SA2 website
Help: SA2 forums

This page is the main entry point to the entire SA2 documentation. You will learn about SA2, how to install the software and its dependencies, and the important concepts that need to be known to use SA2. A quickstart guide will help you to get started with the software. The full documentation (by functionalities, developpers...) is still under development and will be regularly updated.

Table of Contents

About SA2 - top


Screening Assistant (SA) is an academic project started in 2004 in the laboratory of molecular modeling and chemoinformatics (Group Leader: Pr. Luc Morin-Allory) at the Institute of Organic and Analytical Chemistry ( ICOA), UMR CNRS 6005. The first version of SA was developped by Aurélien Monge between 2004 and 2006. The goal was to develop a software specifically dedicated to the management of chemical vendors compounds, and the selection of HTS libraries intended to be screened, using chemoinformatics methods (e.g. diversity, filtering...).

New version

Since then, the software has been completely redesigned to add various chemoinformatics and vizualisation methods. The main idea of this new version is still to perform analysis around chemical libraries, and guide the selection of compounds through both simple interactive visual analysis and more advanced chemoinformatics methods. The software has been completely rewriten to be more flexible and interactive, and to integrate new methods developped in our lab.

Here is a list of the main functionalities available in SA2:

  1. Store you molecules in a MySQL Database. Duplicates are removed using the IUPAC InChI identifier
  2. Associate your molecules to Providers and Libraries
  3. Create new libraries using scaffolds, filtering, diversity analysis...
  4. Compute descriptors, fingerprints and HTS flags
  5. Store and organize any properties associated with molecules
  6. Interactive vizualisation through simple plots or PCA analysis (DRCS methodology)
  7. Perform scaffolds analysis
  8. Reporting: descriptors distribution, comparative statistics...
  9. Search your database: name, substructure, SMARTS, similarity ...


The project is hosted on a sourceforge server. A forum has been setup if you have any problem or question about the software, and a newsletter is also available to keep informed of last news and new releases.
Although posting in the forum is quite easy, it is nevertheless a good idea to use the Bug report system to report crashes in a more consistant and tractable way.

Note that currently, you can post a message in the help forum even if you are not registered. In such case however, you will have to wait for the message to be approved by the administrator. Create a new account if you want to avoid this delay.

Important notes - top

SA2 is an application that stores your data in a database environment. Databases are usually used for static data, typically updated periodically only by database administrators.

SA2 on the contrary, has been developped to provide flexibility from various point of views: the possibility to compute several fingerprints, the possibility to use your own substructure fingerprint, to edit the SMARTS used for HTS flags...

In other words, with the current version of SA2 you are both administrator and user, which means you are the person that select which data will be computed and stored, which data should be modified and eventually recalculated...

As a consequence, there are various things you should be aware of. Here are some typical examples illustrating this point:

We should certainly think of a way of separating the administration tasks from the user tasks. But currently, that's how it works. :)

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