A CoMFA Web Application

in collaboration with

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).

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Dear 3D-QSAR.com user,
unfortunately due to technical failures we had a problem at our database, therefore some data got lost. You may also experience to have your personal account lost. We are sorry and apology for any caused inconvenience. We are doing our best to offer a free 3D QSAR service for not profit or academic organizations. This is an experimental portal and it will become a professional one soon as the under preparation article will be submitted and published.

The 3D-QSAR.com Team