What software is there available for quantitative structure–activity relationship (QSAR) pharmacological studies?
On the G6G Directory of OMICS and Intelligent software, I searched for "QSAR Analysis, and received two product abstracts:

1) SYBYL®-X Suite which contained:


3D QSAR: use the power of industry leading CoMFA in a new way to
generate novel ideas for R-groups - predict the level of biological
activity or potency based on structure-activity data, Not just yes/No
activity predictions;
Cheminformatics: produce highly focused queries that avoid false
positives using a rich set of 3D queries; on-the-fly conformational
searching means you only store a single conformation of your
molecules, keeping database size small and very transportable; and...

Link to this abstract:
http://g6g-softwaredirectory.com/bio/proteomics/structure-modeling/20710-Tripos-SYBYL-X-Suite.php


2) Fujitsu GhostMiner 

GhostMiner can be employed in a number of business intelligence areas and the following areas:


Bioinformatics - genetics, proteomics, Quantitative Structure
Activity Relationship (QSAR) modeling...

Link to this abstract:
http://g6g-softwaredirectory.com/ai/neural-networks/20154-FQS-Poland-Fujitsu-GhostMiner.php


Perhaps the above will help.