The software should work like this: I choose a molecule; and then the software scans a whole library of many many molecules, and then it quantifies the overlap of each one of them with my target molecule. Finally, I can explore the conformations of those molecules with maximum overlap. Hence, I think this is not about docking.
I think you can try UCSF's ZINC database for small molecule structural similarity search. (http://zinc.docking.org/search/structure.php) . Paste SMILES format or draw the structure and search.
Ruhul, it worked well! There is only a minor concern with the fact that the software is integrated in the web database, and the (minor) problem of this is the fact that I have no control of the software.
I tend to prefer applications that are really 'free software', and this means having the source code and be able to modify (and redistribute if wished). In this case, regardless if the ZINC-software employed is or not 'free software', the fact that is wrapped in a web server makes it 'privative software' for any user, hence although I can use the executable freely it does not really qualify as 'free software'.
ok, after this little discussion, I thank Ruhul for his nice reply. The question still remains open for further answers by anybody. I'm still willing to test any other (preferably 'free') software that could be kindly suggested.
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