From fant at pobox.com Mon Aug 6 13:24:25 2007 From: fant at pobox.com (Andrew Fant) Date: Mon, 06 Aug 2007 16:24:25 -0400 Subject: [Zinc-fans] Indiscriminate Binders? Message-ID: <46B78379.2030402@pobox.com> I know that this is kind of the opposite of what virtual screening types normally look for, but has anyone ever generated a subset of zinc compounds that are promiscuous binders? I have a small project going involving binding site prediction, and I could really use a set of likely false positives that would still look lead-like. If anyone has any suggestions, I would be most grateful. Thanks, Andy From jji at cgl.ucsf.edu Tue Aug 7 17:24:21 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 07 Aug 2007 17:24:21 -0700 Subject: [Zinc-fans] Indiscriminate Binders? In-Reply-To: <46B78379.2030402@pobox.com> References: <46B78379.2030402@pobox.com> Message-ID: <46B90D35.1090602@cgl.ucsf.edu> Hi Andy Thanks for your email. We generally consider promiscuous binders (aggregators) to be trouble, so we prefer to filter them out of our libraries and our docking hit lists. I think more useful for the purposes you state - decoys - would be to use DUD - our directory of useful decoys, on the web at http://dud.docking.org and described in our J Med Chem paper last year: Huang N, Shoichet BK* and Irwin JJ*, "Benchmarking Sets for Molecular Docking", J. Med. Chem, 2006, 49(23), 6789-6801 (DOI ). I hope you find this helpful. Best wishes, John Andrew Fant wrote: > I know that this is kind of the opposite of what virtual screening types > normally look for, but has anyone ever generated a subset of zinc compounds that > are promiscuous binders? I have a small project going involving binding site > prediction, and I could really use a set of likely false positives that would > still look lead-like. If anyone has any suggestions, I would be most grateful. > > Thanks, > Andy > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From jji at cgl.ucsf.edu Wed Aug 8 18:01:04 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 08 Aug 2007 18:01:04 -0700 Subject: [Zinc-fans] Ph filter In-Reply-To: <200706190057.l5J0v8AY014232@cruncha.qtp.ufl.edu> References: <200706190057.l5J0v8AY014232@cruncha.qtp.ufl.edu> Message-ID: <46BA6750.2040200@cgl.ucsf.edu> Hi Lena Thanks for your question and your interest. Sorry to take so long to get back to you. This is a reasonable request. It is an option in our "create subset" option, which unfortunately hasn't ever really worked correctly. I will try to get this done soon. John Lena Dolghih wrote: > hi, > > thanx for such a prompt reply. I have one more question. Is there a way to > select a subset of compounds just of reference pH? > > Lena > > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From jji at cgl.ucsf.edu Wed Aug 8 18:04:20 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 08 Aug 2007 18:04:20 -0700 Subject: [Zinc-fans] schema and data, or ID and SMILES string In-Reply-To: <04bc01c7b1ef$d2c144d0$0e905f0a@universiz0bbss> References: <04bc01c7b1ef$d2c144d0$0e905f0a@universiz0bbss> Message-ID: <46BA6814.7030408@cgl.ucsf.edu> Hi Michael Thanks for your interest in ZINC. Michael K Wasnick wrote: > Hi, > > (I scanned as far back as June 2006, sorry in advance if this question > has already been answered.) > > Is it possible to download the schema and the data for the MYSQL 4.1 > ZINC database? > If not, is it possible to get just a dump of the table that has the > ZINC identifier for each compound and its SMILES string? You can get all ZINC IDs and SMILES strings in the "everything subset". http://zinc.docking.org/subset1/10/10_p0.smi.gz > > My interest is to integrate the ZINC data into with other data that we > have in-house, and the main piece of functionality that I need to > build (or modify if someone else built it and it is available) is to > be able to do a substructure search of ZINC behind our firewall. I hope the above file will work for you. Sorry to take so long to get back to you. John From jji at cgl.ucsf.edu Mon Aug 13 14:57:30 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Mon, 13 Aug 2007 14:57:30 -0700 Subject: [Zinc-fans] Ph filter In-Reply-To: <200706190057.l5J0v8AY014232@cruncha.qtp.ufl.edu> References: <200706190057.l5J0v8AY014232@cruncha.qtp.ufl.edu> Message-ID: <46C0D3CA.7060506@cgl.ucsf.edu> Hi Lena Sorry to be so slow getting back to you. You can download molecules for the pre-made subsets (by vendor or by physicochemical properties) as a single representation at pH 7. hope this helps. John Lena Dolghih wrote: > hi, > > thanx for such a prompt reply. I have one more question. Is there a way to > select a subset of compounds just of reference pH? > > Lena > > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From jji at cgl.ucsf.edu Mon Aug 13 15:12:02 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Mon, 13 Aug 2007 15:12:02 -0700 Subject: [Zinc-fans] re Searching ZINC for Supplier Catalog numbers In-Reply-To: <58F49C25B66F4C4DA7FE79B9E79C89B981971C@exvicn1-mel.nexus.csiro.au> References: <58F49C25B66F4C4DA7FE79B9E79C89B981971C@exvicn1-mel.nexus.csiro.au> Message-ID: <46C0D732.8040902@cgl.ucsf.edu> Hi Vidana Thanks for your query. Sorry to take so long to respond. We do not support queries against multiple supplier constraints at this time. Sorry. John Vidana.Epa at csiro.au wrote: > > Hi John, > > > > From the ZINC search page, it doesn?t look as if one can > submit a list of Supplier Catalog numbers (for a selected supplier) to > be searched (the way one can submit a list of ZINC codes). Can one do > the former, instead of searching for one catalog number at a time? > > > > Thanks. > > > > Cheers, > > > > Vidana. > > > > > > > > Vidana C. Epa > > > > CSIRO, > > Division of Molecular Health & Technologies, > > 343 Royal Parade, > > Parkville, Victoria 3052, > > AUSTRALIA. > > > > tel: (61) - 3 - 9662 - 7345 > > fax:(61) - 3 - 9662 - 7347 > > > > email: Vidana.Epa at csiro.au > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From rafi4dd at gmail.com Wed Aug 22 11:00:05 2007 From: rafi4dd at gmail.com (rafi A) Date: Wed, 22 Aug 2007 14:00:05 -0400 Subject: [Zinc-fans] Clustering and measuring diversity -reg Message-ID: <2bdc62b30708221100y2d9de1fcy385006b1085ce9f2@mail.gmail.com> Hello, I am new to this group. First of all I wish to thank the people for creating Zinc database, which I find very helpful in virtual screening. I have few basic questions. If we select a database for virtual screening, how should we analyze the properties of the database? Is there any parameters which should be looked into. My other question is: How is the diversity of the databases analyzed? Can anyone give me some idea about the tanimoto and how it is measured. Is there any free software by which we can cluster the database and also study the diversity. Or is there any approach to do a clustering analysis and take representative examples from each cluster and study it by further docking. Sorry for asking lot of question. But your reply will be very helpful. Thanks, Rafi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20070822/cc403e6e/attachment.html From jji at cgl.ucsf.edu Thu Aug 23 11:41:16 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Thu, 23 Aug 2007 11:41:16 -0700 Subject: [Zinc-fans] Clustering and measuring diversity -reg In-Reply-To: <2bdc62b30708221100y2d9de1fcy385006b1085ce9f2@mail.gmail.com> References: <2bdc62b30708221100y2d9de1fcy385006b1085ce9f2@mail.gmail.com> Message-ID: <46CDD4CC.6040401@cgl.ucsf.edu> Hi Rafi Thank you for your email and your interest in ZINC. > > I have few basic questions. If we select a database for virtual > screening, how should we analyze the properties of the database? Is > there any parameters which should be looked into. We do some basic property distribution analysis, which we attempt to economically compress into four scatterplots. For example, see the "lead like subset" graphs here... http://zinc.docking.org/subset1/1/index.html You may also download the properties at http://zinc.docking.org/subset1/1/1_prop.xls and use gnuplot (or whatever) yourself. > > My other question is: How is the diversity of the databases analyzed? > Can anyone give me some idea about the tanimoto and how it is measured. We have our own statistics for "diversity" which we provide. We use SUBSET 1.0 to pick cluster representatives from a low-to-high molecular weight sorted list. We cluster at 90, 80, 70, and 60 % Tanimoto circles from the representatives. This gives you some idea of the amount of "chemical similarity" present in the collection, but it is just one of many ways to do it. To know more about Tanimoto, please look at the Daylight Theory Manual (google it). > > Is there any free software by which we can cluster the database and > also study the diversity. Or is there any approach to do a clustering > analysis and take representative examples from each cluster and study > it by further docking. SUBSET 1.0 is free. (from Marc Nicklaus's lab). I suspect our approach is not viewed as orthodox by the leading practitioners in the field of similarity clustering. The thing to ask youself is: what is the question? What do you think you are measuring or estimating with "diversity". > > > Sorry for asking lot of question. But your reply will be very helpful. I am happy to be asked questions, particularly ones I have a reasonable shot at answering. ;-) > > > Thanks, > Rafi > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From Filippo.Marchioni at cchmc.org Fri Aug 24 05:36:33 2007 From: Filippo.Marchioni at cchmc.org (Filippo Marchioni) Date: Fri, 24 Aug 2007 08:36:33 -0400 Subject: [Zinc-fans] vendor Message-ID: Dear all, I have a question regarding a vendor. I am trying to contact ChemStar about some chemicals from their database but so far I wasn't able to reach them. I have these informations: email: chemstar at online.ru or chemstar at chemstarionline.com (this one is not working) phone number 7 095 977 9811 does anybody know if they are still on business and how to reach them? Thanks for your help Best Filippo