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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Do you want to learn more on 3-D QSAR?
Attend Designᴵᵀ-TO-LEAD


1st Computational Medicinal Chemistry Workshop
September 3rd - 8th, 2018
Kragujevac, Serbia

Designᴵᵀ-TO-LEAD is the specialized WorkShop, organized in City of Kragujevac, Republic of Serbia, with the aim to contribute in spreading knowledge in the field of Medicinal Chemistry and Rational Drug Design by means of employment of computer and computational techniques.

Designᴵᵀ-TO-LEAD is structured for students of Chemistry, Pharmacy, and Pharmaceutical Biotechnology, PhD students and PostDoc of all disciplines involved in Medicinal Chemistry, as well as for Academics and industry involved in providing medicinal and pharmaceutical services. The contribution of computational methodologies to drug discovery is no longer a matter of dispute and all major World’s pharmaceutical and biotechnology companies use computational design tools. Computer-aided drug design encompasses computational methods and resources that are used to facilitate the design and discovery of new bioactive chemical entities.

Designᴵᵀ-TO-LEAD will cover the main computational techniques currently used in the drug discovery, process supplying a basic level of knowledge of this field. All the thought computational approaches will focus mainly on the development of three-dimensional quantitative structure-activity relationships (3-D QSAR) and related tools.

Designᴵᵀ-TO-LEAD will be divided into theoretical lesson and practical sessions with the aim to allow the participants to independently apply the computational techniques to their own home projects.