Pipeline Pilot would be great for reasonably lazy people. A combination of Dragon (descriptor calculation) + R (data modeling) is for more statistics-savvy, command-line folks.Add your answer

You can calculate a lot of 1D, 2D, 3D, 4D descriptors using on-line computations at www.chemosophia.com such as molecular volume, surface, non-polar, positively and negatively charged areas, etc., etc., etc. now for free. Additionally You can calculate there a lot of physicochemical properties. Besides, you can calculate hundreds descriptors related with molecular shape using "Calculation of descriptors" software in the same services or in "Calculation of descriptors and molecular superimposition" service at www.chemosophia.com .

you could use CORAL and SARpy software:

http://www.vega-qsar.eu/research.html

Antonio Cassano sir, i have used vega to check the mutagenicity, carcinogenicity, log P values etc. but i don't know how it can be used to do QSAR?

If you have some computer science background you can use some generic tools to build the models.

When you have computed your molecular descriptors (features) as before indicated, you can use a classical modelling approach that requires to  select  the descriptors, divide data into training and test set,   construct the model(s) with the training set,  validate on the test set.

A powerful generic and free tool is WEKA, http://www.cs.waikato.ac.nz/ml/weka/downloading.html

that contains many methods, linear and non linear,  but requires some training

A commercial tool is Matlab and related toolbox, that requires training too.

If you want to build a SAR model, you can directly use a free tool as SARpy just entering a file with the SMILES and the property  of interest.