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
What are you actually trying to achieve? Your question is extremely vague.

Do you just want a big collection of drug-like molecule? Grab <a href="http://www.gdb.unibe.ch/gdb/home.html">GDB-17</a>

Do you want a curated source of biologically interesting molecules? Go to <a href="http://www.ebi.ac.uk/chebi/">ChEBI</a>

Do you want small molecules with annotated activity? Try <a href="https://www.ebi.ac.uk/chembldb/">ChEMBL</a>

Do you want small molecules bound to a protein? Try <a href="http://www.rcsb.org/pdb/home/home.do">PDB</a>

For docking, just go to any literature search engine and search for small molecule docking. You will get reviews, algorithms and papers describing software. There is plenty of literature, so start reading.

Edit: After several comments, it seems the interest lies in identifying any compound which may inhibit the activity of the given receptor. For this purpose I would suggest using <a href="http://zinc.docking.org/">ZINC</a>, which also has vendor information.