On Sun, Dec 29, 2019 at 9:31 PM suyash pant <suyashni...@gmail.com> wrote:
> Thanks for the tip! > This is working well for me. > Another thing I want to know. Well I need to filter my data gor virtual > screening. As we don't have much computation resources for going with large > number of molecules, so we decided to go with similarity search first then > with structure based docking. > So how much this will be reliable and will it be a good starting point? > Thank you > The eMolecules free database is also a database of commercially available compounds, but eMolecules does not include "virtual" compounds that are not actually in stock, nor do we include compounds from unreliable suppliers. For example, some suppliers advertise large catalogs, but when you actually try to order, up to 90% of the compounds are not in stock. The Zinc database is an excellent resource, but it contains over 200 million compounds. There simply are not this many chemical compounds in stock rooms around the world; many of these 200 million compounds are "virtual", compounds that have never been synthesized. If you order these virtual compounds, delivery is 12-20 weeks with significant failure rates (predicted synthesis by the supplier fails or yields are too low). eMolecules has about 7.4 million building-block compounds in our catalogs, and 19.1 million screening compounds. From actual ordering data, we know that these are realistic numbers for chemicals that can be delivered reliably. We process hundreds of orders per day, so we know exactly which suppliers are reliable and which are not. We don't include the unreliable suppliers, nor do we include catalogs of "virtual" compounds from reliable suppliers. If commercial availability of these compounds is important, you might want to start with eMolecules' free downloads database: https://downloads.emolecules.com Best, Craig > On Sun, 29 Dec, 2019, 11:59 Craig James, <cja...@emolecules.com> wrote: > >> >> >> On Fri, Dec 27, 2019 at 7:48 AM suyash pant <suyashni...@gmail.com> >> wrote: >> >>> Hello sir/mam >>> I hope You are doing well >>> I am writing this mail, as I am facing certain problem with doing the >>> similarity search using "Openbable" >>> I have a zinc dataset for lead like and drug like molecules. >>> Unfortunately I am not able to go with structure based docking for the >>> complete dataset. Similar like zinc dataset I have some more dataset and I >>> want to further proceed with tanimoto similarity search first to filter and >>> reduce the dataset for my virtual screening and docking. >>> Now here when I am taking my reference structure (smilies) for >>> similarity search using command *"babel mymols.fs results.sdf >>> -sCC1=CC=C(C=C1)C2=C(C=C(C=C2)F)COC3=CC=C(C=C3)CCC(=O)O -at0.6"* So I >>> want why I am getting a syntex error and when I am taking same smilie code >>> mentioned in your website it is giving. Is there any problem with my smilie >>> code or I am doing something wrong? >>> >> >> I assume you are using Linux or a Unix-like operating system such as a >> Macintosh. In that case, you must use quotes around the SMILES, because it >> contains special characters that the command-line shell tries to interpret. >> Try this command with the quotes exactly as shown: >> >> babel mymols.fs results.sdf >> -s"CC1=CC=C(C=C1)C2=C(C=C(C=C2)F)COC3=CC=C(C=C3)CCC(=O)O" -at0.6 >> >> >> Craig >> >> >> Kindly, provide the needful assistance for the mentioned issue. >>> Thank You >>> >>> Suyash Pant >>> Research Scholar, >>> NIPER, Kolkata >>> Department of Pharmacoinformatics >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >> >> >>
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