Hi. Warm greetings. I am senthilperiyasamy, research scholar. Recently I have synthesized some 1,2,4-oxadiazole molecules without targeting particular diseases.
Target is unknown for them and went hunting on SWISS target prediction. I got results for all and for instance to one molecule as in the attachment.
The doubt is:
How to find the Protein ID from the list of targets?
Each genetic code contains several Proteins. So how to proceed further?
your guidance might be helpful for us.
Collaborations are welcome.
Thanks & Regards
Senthil.P.
Mob:7204263360
Hi Senthil,
You can search your genetic codes in Uniprot.
http://www.uniprot.org/
PDB_id will be shown, if available.
Dear Yoshinobu
Hi.Thanks for your kind reply. I found the protein ids when I placed genetic codes in uniprot. For example, genetic codes for Spinghosine-1-phosphate receptors [S1P1,S1P2, S1P3, S1P4 & S1P5] found for 15 compounds out of 26 compounds of 1,2,4-oxadiazole analogs.
when I placed the genetic code in Uniprot for these receptors, I got the results and please see in the attachment.
For the S1P receptors, I got these protein ids. which protein among them I select for docking? is it possible for docking on multiple proteins at the same time?
Please provide your valuable guidance and very thankful in advice.
Regards
Senthil
Hi Senthil,
It may not be possible to do multiple receptors docking, because the atom coordinates of the protein structures should be different among them. Simply, you can do docking against each structure of the proteins. It's not tedious by use of AutoDock Vina and/or LeDock.
http://vina.scripps.edu/
http://www.lephar.com/software.htm
Multiple ligands docking using AutoDock Vina can be done by a Unix/Linux shell script. Check my answers in the following ResearchGate post:
https://www.researchgate.net/post/How_to_do_virtual_screening_of_a_library_of_ligands_through_autodock_Vina
LeDock is designed for multiple ligand docking.
Please check the answers here in this link which might be helpful to you:
https://www.researchgate.net/post/Can_anyone_help_me_with_the_following_How_can_someone_know_the_target_protien_for_a_specific_drug_in_order_to_perform_molecular_docking?
Dear Dr. Yoshinobu
Great Morning. Thank you so much for your valuable guidance. I will go with the Le dock for multiple ligand docking.
Regards
Senthil
Dear Dr. Mostafa
Great morning. Thanks for your kind reply and valuable information.
Really helpful in prediction of the protein targets.
Regards
Senthil
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