Home
This Title All WIREs
WIREs RSS Feed
How to cite this WIREs title:
WIREs Comput Mol Sci
Impact Factor: 8.836

Two personal perspectives on a key issue in contemporary 3D QSAR

Full article on Wiley Online Library:   HTML PDF

Can't access this content? Tell your librarian.

Chemists working with small molecules are under enormous pressure to be able to reliably predict how biological systems in particular and the environment in general will respond to the deployment of the corresponding compounds as medicines, cosmetics, or in other manufactured goods. To be specific and robust, any such prediction must be based on an implicit or explicit mathematical model of how chemical structure relates to biological activity—i.e., on some postulated quantitative structure–activity relationship (QSAR). Such models are necessarily limited in how broadly they can be applied. Their applicability domain depends on the structural diversity of the data set used, but also on the descriptors used to characterize how that structural variation relates to the activity in question. In principle, descriptors based on the molecular interaction fields produced by atoms distributed in three‐dimensional (3D) space should be the most general of all, but finding suitable conformations and alignment is a challenge. One way to obtain these is by taking the structure of the macromolecular target into account as well, as is done in scoring ligand/receptor complexes for virtual screening. Unfortunately, the available docking tools are generally not up to the task. Here, we share some personal observations and opinions on two possible ways to address this shortcoming: implicitly, by iterative rescoring of docked poses obtained using derived 3D QSARs; and explicitly, by evaluating ligand interaction fields with respect to target atoms rather than against generalized probe atoms. © 2011 John Wiley & Sons, Ltd.

This article is categorized under:

  • Computer and Information Science > Chemoinformatics

Browse by Topic

Computer and Information Science > Chemoinformatics

Access to this WIREs title is by subscription only.

Recommend to Your
Librarian Now!

The latest WIREs articles in your inbox

Sign Up for Article Alerts