Dear All,

I have to deal some small molecules screening for my protein-drug docking studies. Please suggest me few small molecule databases ..also the free software can use to screen them...thank you
As you suggested, you will find a smaller but usefully target mapped compound and drug set at <a href="http://www.guidetopharmacology.org/?">http://www.guidetopharmacology.org/</a>

You should probably start docking with PDB structures anyway so you can get a small set from the above by using the PubChem query

https://www.ncbi.nlm.nih.gov/pccompound?term=%28%231%29%20AND%20pccompound_structure[filt]%20AND%20%22IUPHAR/BPS%20Guide%20to%20PHARMACOLOGY%22[SourceName]&cmd=DetailsSearch=872