What are you actually trying to achieve? Your question is extremely vague.
Do you just want a big collection of drug-like molecule? Grab GDB-17
Do you want a curated source of biologically interesting molecules? Go to ChEBI
Do you want small molecules with annotated activity? Try ChEMBL
Do you want small molecules bound to a protein? Try PDB
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 ZINC, which also has vendor information.
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David Westergaard
Fine...
The protein sequences I am planning to work with, do not have any available structure. So I am developing a molecular modeling based study first then the screening of molecules to dock with the predicted model. So what kind of molecular databases suit to this?
What is your goal? Do you just want to find some compounds that bind? Do you want to find already FDA approved drugs which bind? Do you want to find potential bacterial metabolites binding to the protein?
A word of advice: Before starting a project like this, have a clear plan for what you want to study and what you are hoping to find. I do not understand what you mean by "So I am developing a molecular based study first then the screening of molecules to dock with the predicted model". What is a "molecular based study"? Are you testing the compounds in the lab prior to the in silico studies?
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David Westergaard
M goal of work is to determine few novel molecules which can inhibit the activity of the receptor of interest..( determining potential compounds that can be taken for clinical trial), that need not be FDA approved or already known drugs..the study I would like to follow is molecular modeling based ( sorry for not to add modeling in earlier ).
Thanks for the suggestions!
As you suggested, you will find a smaller but usefully target mapped compound and drug set at http://www.guidetopharmacology.org/
You should probably start docking with PDB structures anyway so you can get a small set from the above by using the PubChem query
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Abdul Rafay Khan
If you are looking for an easy-to-use and efficient tool for quick virtual screening, you can also try Molecular Docking Online. It’s a great free alternative for performing online molecular docking studies without complex local installations
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In general you should not ask two questions in one post. But I particularly like to ask you what information you would like to get from the database? If you need structures, why not just use ChemSpider or PubChem?
If the person setting you the assignment has not given proper guidence and context for this (e.g. explained about PubChem) or expects you to magic up free docking - they ought to have (to put it politely)
You can try https://mcule.com/apps/1-click-docking/ to get some nice pictures at least
Can I search the molecules from http://www.guidetopharmacology.org/?