Hi Arun,

I guess that very much depends on the type of analysis you want to carry out. To be able to handle a large number of compounds platforms like Pipeline Pilot or Knime are essential (see links).

From a visualisation point of view you might be interested in Scaffold Hunter  (http://scaffoldhunter.sourceforge.net/).

And if you are into large chemical space you might find this also interesting:

http://pubs.acs.org/doi/pdf/10.1021/ar500432k

Hope it helps.

Kind regards

https://www.knime.org/

http://accelrys.com/products/pipeline-pilot/

Hi,

For general purpose visualization you have Visit (with parallel computing): https://wci.llnl.gov/simulation/computer-codes/visit/

But you're probably looking for something more oriented such as Gephi: http://gephi.github.io/

Both software claim to be able to handle a lot of data if you have the computer(s) for it.

Didn't knew Scaffold Hunter. I'll take a look into it.

Dear Fabio , thankyou for your suggestion  

scaffold hunter is good , i used it before to find common scaffold for a small dataset.

The ACR paper is interesting and i would like to do such visualization of chemical space of large datasets.

Have you used MQN applet and if so did you modify it accordingly ?

Dear Pedro 

thankyou for ur suggestions , i ll look into GEPHIS and VisIT