Question: Small molecule databases
1
gravatar for Sabine
5.0 years ago by
Sabine60
India
Sabine60 wrote:

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

 

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Sabine60
2

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?

ADD REPLYlink written 5.0 years ago by Egon Willighagen5.2k
2

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

 

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by cdsouthan1.8k

can i search the molecules from http://www.guidetopharmacology.org/?

ADD REPLYlink written 5.0 years ago by Sabine60
4
gravatar for David Westergaard
5.0 years ago by
Copenhagen, Denmark
David Westergaard1.4k wrote:

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.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by David Westergaard1.4k
3
gravatar for Denise - Open Targets
5.0 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

You may want to have a look at ChEMBL (database of bioactive drug-like small molecules) and ChEBI too! 

ADD COMMENTlink written 5.0 years ago by Denise - Open Targets5.0k
3
gravatar for cdsouthan
5.0 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

As you suggested,  you will find a smaller but usefuly 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

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

 

 

ADD COMMENTlink written 5.0 years ago by cdsouthan1.8k
2
gravatar for Sabine
5.0 years ago by
Sabine60
India
Sabine60 wrote:

fine...

the protein sequences i am planning to work with , doesnot 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?

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Sabine60
1

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?

 

ADD REPLYlink written 5.0 years ago by David Westergaard1.4k
1
gravatar for Abdul Rafay Khan
5.0 years ago by
Karachi, PK
Abdul Rafay Khan1.0k wrote:

https://www.ebi.ac.uk/chebi/aboutChebiForward.do

ADD COMMENTlink written 5.0 years ago by Abdul Rafay Khan1.0k
1
gravatar for Sabine
5.0 years ago by
Sabine60
India
Sabine60 wrote:

my 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!

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Sabine60

See edit to my previous answer.

ADD REPLYlink written 5.0 years ago by David Westergaard1.4k

Tell us the receptor then we can make more tangible suggestions but I dont think you'll be going for clinical trials off the bat

ADD REPLYlink written 5.0 years ago by cdsouthan1.8k
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