Three-dimensional quantitative structure-activity relationships (3-D QSAR) involve the analysis of the quantitative relationship between the biological activity of a set of compounds and their three-dimensional properties using statistical correlation methods.
On June 18, 2011 Comparative Molecular Field Analysis (CoMFA) patent has dropped any restriction on the use of GRID and partial least-squares (PLS) technologies and the Rome Center for Molecular Design (RCMD) team headed by Prof. Rino Ragno has opened an alpha version of a 3D QSAR web server (www.3d-qsar.com) based on the 3-D QSAutogrid/R engine. After a few years here you have landed in the a web application to build 3-D QSAR models based on the same CoMFA settings: TRIPOS force field based molecular interaction fields (MIFs) and PLS statistical engine.
This is an experimental but complete version that relies on already aligned data set (a Py-Align web application is under development). The molecules can be assigned to training and test sets and by a simple setting page the CoMFA model can be easily build and graphically inspected by several MIF contour plots and tables.
As of January 2017 a full 3-D QSAR portal is available in www.3d-qsar.com. You can draw a training set of molecule, insert their biological activity, make conformational analysis with three different methods, align the conformation using two different methods and several alignment rules, build a 3-D QSAR model by tuning sevela settings, get the statistical results and view different 3-D QSAR maps and download the images. All for free.
We are continuously working on the 3-D QSAR portal. At the moment calculations are highly reliable, more features will be added in the near future.
After you have registered two pre-loaded data sets will be available in your area, namely these are the original CoMFA steroid training set (JACS 1988) and the DOT1L training set (Poster #164 at XXI EuroQSAR meeting by Manuela Sabatino, Alexandros Patsilinakos and Rino Ragno).