[Zinc-fans] Zinc-fans Digest, Vol 37, Issue 1
Walter Novak
wnovak at brandeis.edu
Wed Jul 30 05:42:03 PDT 2008
Hi Jian,
I would try Pubchem (http://pubchem.ncbi.nlm.nih.gov/) or Scifinder.
Best,
Wally
On Jul 30, 2008, at 8:31 AM, jianping zhou wrote:
> Hi,
>
> I am new here. I can download molecules in SMILES or SDF format, but
> if I need more information such as compound name, IUPAC name,
> formula, and structure etc.., what would be the best way to get thse
> information?
>
> Thanks,
>
> -jian
>
> --- On Mon, 6/16/08, zinc-fans-request at docking.org <zinc-fans-request at docking.org
> > wrote:
> From: zinc-fans-request at docking.org <zinc-fans-request at docking.org>
> Subject: Zinc-fans Digest, Vol 37, Issue 1
> To: zinc-fans at docking.org
> Date: Monday, June 16, 2008, 7:52 AM
>
> Send Zinc-fans mailing list submissions to
> zinc-fans at docking.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>
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> or, via email, send a message with subject or body 'help' to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Zinc-fans digest..."
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>
> Today's Topics:
>
> 1. Re: total number of compounds in vendors subset -reg
> (John J. Irwin)
> 2. Re: All-purchasable subset (John J. Irwin)
> 3. non-unique ZINC ids in Zinc7 (Jens Auer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 28 May 2008 07:30:06 -0700
> From: "John J. Irwin" <jji at cgl.ucsf.edu>
> Subject: Re: [Zinc-fans] total number of compounds in vendors subset
> -reg
> To: rafi A <rafi4dd at gmail.com>
> Cc: zinc-fans at docking.org
> Message-ID:
> <483D6C6E.1070101 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Rafi
>
> Thanks for your email and your interest in ZINC. Sorry to take so long
> to get back to you.
>
> I have recently exported a fresh copy of Sigma Aldrich in ZINC 8
> (http://zinc8.docking.org). There are 17,931 molecules in the source
> catalogs, and 15186 in ZINC. We downloaded every SDF file we could
> find
> on the Sigma Aldrich website. I've ordered the CD, and will include
> any
> additional molecules that may be there.
>
> Previously we have included the "rare" library from Sigma Aldrich,
> based
> on files we received perhaps 5 years ago. There were nearly 200K of
> these. Since these are no longer available on the Sigma Aldrich
> website,
> they have been removed from ZINC. I think this change may account for
> some of the discrepancies you saw.
>
> Good luck
>
> John
> UCSF ZINC
> Team
>
>
>
>
> rafi A wrote:
> > Hello,
> >
> >
> > Where can we find the total number of compounds in a subset?
> >
> >
> >
> > For example I want to download the vendors/sigma Aldrich subset.
> >
> >
> >
> > In the table column, catalog information: Source entries; shows
> 295,562.
> >
> > Another column, ZINC information: Loaded; shows 115,595. So I
> expected
> > the total number of molecules to be either 295,000 or 115,000.
> >
> >
> >
> > But when I downloaded the mid pH,( SMILES or mol2) it shows only
> > 14,449 molecules.
> >
> >
> >
> > Did I misunderstood something. Or can you tell me where I can find
> the
> > total number of molecules in a subset before downloading.
> >
> >
> >
> > Thanks in advance.
> >
> >
> >
> > Best regards,
> >
> >
> Rafi
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 28 May 2008 08:04:29 -0700
> From: "John J. Irwin" <jji at cgl.ucsf.edu>
> Subject: Re: [Zinc-fans] All-purchasable subset
> To: "Josmar R. da Rocha" <bije_br at yahoo.com.br>
> Cc: zinc-fans at docking.org
> Message-ID: <483D747D.6000107 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi Josmar
>
> I have exported "all purchasable" for ZINC 8, which now has 8.4M
> molecules. It should have nearly 10M in a month or so after I get a
> few
> more problems sorted out.
>
> May I take this opportunity to point out that we have created several
> fun new subsets in ZINC that we have found useful, and you may too!
>
> #17 - neutral fragments. (51K of these)
> #29 - CNS permeable (209K of these)
> #33 - goldilocks - not too big, not too small, not too polar, not too
> greasy - just right. (almost 500K of
> these)
> #50 - stiff-solubles - fairly rigid fragments that are probably quite
> soluble.
>
>
> Happy docking!
>
> John
> UCSF ZINC Team
>
>
> Josmar R. da Rocha wrote:
> > Dear Zinc-fans,
> >
> > I noticed that the subset "all-purchasable" that could be
> downloaded
> > from Zinc 7 is no longer available in Zinc 8. I'd Like to know if
> the
> > only way to get this subset would be by downloading each one of the
> > files found in " By vendor /in stock" subsets or is there any
> other way?
> >
> > Thanks in advance!
> >
> > Josmar Rocha
> >
> >
> ------------------------------------------------------------------------
> > Abra sua conta no Yahoo! Mail
> >
> <http://br.rd.yahoo.com/mail/taglines/mail/*http://br.mail.yahoo.com/
> >,
> > o ?nico sem limite de espa?o para armazenamento!
> >
>
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Zinc-fans mailing list
> > Zinc-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 11 Feb 2008 11:49:57 +0100
> From: Jens Auer <auer at bit.uni-bonn.de>
> Subject: [Zinc-fans] non-unique ZINC ids in Zinc7
> To: zinc-fans at docking.org
> Message-ID: <1202726997.9493.14.camel at lsi-08>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> we have just found several molecules in the Zinc7 database which are
> different in structure but have the same ZINC id. I've compiled a list
> of ids where you find different compounds (acc. to a unique SMILES
> string computed with MOE) under each id. As an example, I've also
> attached two compounds with id ZINC00000308 where you can
> see that they
> really differ in structure.
>
> Best regards,
> Jens
>
> --
> Jens Auer
> Life Science Informatics
> B-IT Intl. Center for Information Technology
> Rheinische Friedrich-Wilhelms-University Bonn
> Dahlmannstra?e 2
> D-53113 Bonn
> phone: +49 (228) 2699 314
> email: auer at bit.uni-bonn.de
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> ZINC00000308
> MOE2007 3D
>
> 55 58 0 0 1 0 0 0 0 0999 V2000
> 7.0050 11.3100 -1.5430 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.8640 11.9320 -0.7350 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.5060 12.0740 -2.7340 C 0 0 0 0 0 0 0 0 0 0 0
> 0
> 4.3760 13.5990 -2.7240 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.3480 10.1300 -1.3000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.1840 9.6930 0.1580 C 0 0 3 0 0 0 0 0 0 0 0 0
> 5.0500 10.0170 0.7340 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.0700 8.1920 0.2220 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.8500 7.5840 0.2470 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.7690 6.1840 0.3070 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.8520 5.4310 0.3440 N 0 0 0 0 0 0 0 0 0 0 0 0
> 5.0730 5.9720 0.3160 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.2210 7.3810 0.2560 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.5080 7.9410 0.2330 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.5990 7.1270 0.2680 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.4550 5.7420 0.3270 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.2230
> 5.1640 0.3510 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4360 5.5360 0.3340 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.2760 6.3280 0.3010 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.9570 5.7590 0.3250 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0840 4.3590 0.3840 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.3490 3.7470 0.4090 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.4400 2.3900 0.4610 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.2960 1.5940 0.5000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0550 2.1520 0.4770 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0790 3.5500 0.4180 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.3440 4.1580 0.3930 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0020 10.2840 0.7020 O 0 0 0 0 0 0 0 0 0 0 0 0
> 7.9500 11.4750 -1.0250 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.8330 10.2390 -1.6500 H
> 0 0 0 0 0 0 0 0 0 0 0 0
> 7.0460 11.7720 -2.5290 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.9770 13.0160 -0.7230 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.8930 11.5520 0.2860 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.4110 11.7910 -3.2700 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.6380 11.6390 -3.2300 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.4840 13.8840 -2.1650 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.2560 14.0360 -2.2520 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.2950 13.9640 -3.7480 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.1980 9.6110 -1.7410 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.4440 9.8860 -1.8560 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.9480 8.1780 0.2220 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.6330 9.0130 0.1880 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.5880 7.5590 0.2490 H 0 0 0 0 0 0
> 0 0 0 0 0 0
> 8.3360 5.1170 0.3530 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.1300 4.0890 0.3970 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3660 7.4030 0.2560 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.8400 6.3810 0.2980 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.2440 4.3500 0.3820 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.4130 1.9220 0.4760 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.3960 0.5200 0.5450 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.8230 1.5230 0.5050 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.2390 3.5530 0.4190 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.1900 10.0400 0.2370 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.5580 11.5930 -1.3380 N 0 3 0 0 0 0 0 0 0 0 0 0
> 3.8140 12.0510 -0.7990 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 1 29 1 0 0 0 0
> 1 30 1 0 0 0
> 0
> 1 31 1 0 0 0 0
> 2 32 1 0 0 0 0
> 2 33 1 0 0 0 0
> 2 54 1 0 0 0 0
> 3 4 1 0 0 0 0
> 3 34 1 0 0 0 0
> 3 35 1 0 0 0 0
> 3 54 1 0 0 0 0
> 4 36 1 0 0 0 0
> 4 37 1 0 0 0 0
> 4 38 1 0 0 0 0
> 5 6 1 0 0 0 0
> 5 39 1 0 0 0 0
> 5 40 1 0 0 0 0
> 5 54 1 0 0 0 0
> 6 7 1 0 0 0 0
> 6 8 1 0 0 0 0
> 6 28 1 0 0 0 0
> 8 9 2 0 0 0 0
> 8 13 1 0 0 0 0
> 9 10 1 0 0 0 0
> 9 41 1 0 0 0 0
> 10 11 2 0 0 0 0
> 10 18 1 0 0 0 0
> 11 12 1 0 0 0 0
> 12 13 1 0 0 0 0
> 12 17 2 0 0 0 0
> 13 14 2 0 0 0 0
> 14 15 1 0 0 0 0
> 14 42 1 0 0 0 0
> 15 16 2 0 0 0 0
> 15 43 1 0 0 0 0
> 16 17 1 0 0 0 0
> 16 44 1 0 0 0 0
> 17 45 1 0 0 0 0
> 18 19 1 0 0 0 0
> 18 27 2 0 0 0 0
> 19 20 2 0 0 0 0
> 19 46 1 0
> 0 0 0
> 20 21 1 0 0 0 0
> 20 47 1 0 0 0 0
> 21 22 1 0 0 0 0
> 21 26 2 0 0 0 0
> 22 23 2 0 0 0 0
> 22 48 1 0 0 0 0
> 23 24 1 0 0 0 0
> 23 49 1 0 0 0 0
> 24 25 2 0 0 0 0
> 24 50 1 0 0 0 0
> 25 26 1 0 0 0 0
> 25 51 1 0 0 0 0
> 26 27 1 0 0 0 0
> 27 52 1 0 0 0 0
> 28 53 1 0 0 0 0
> 54 55 1 0 0 0 0
> M CHG 1 54 1
> M END
> > <name>
> ZINC00000308
>
> $$$$
> ZINC00000308
> MOE2007 3D
>
> 41 42 0 0 0 0 0 0 0 0999 V2000
> 2.4960 4.2870 0.4940 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.1980 3.5220 0.4960 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0830 4.1400 0.7170 N 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0820 5.3400 0.9250 O 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1120 5.9210 1.1480 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1250 5.2510
> 1.1370 O 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1820 7.2460 1.3840 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1.1990 2.0680 0.2440 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4020 1.4000 0.0050 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4000 0.0410 -0.2300 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.2060 -0.6650 -0.2290 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0020 -0.0050 0.0090 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0040 1.3570 0.2460 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1660 -0.7000 0.0090 O 0 0 0 0 0 0 0 0 0 0 0 0
> -2.3720 0.0570 0.1350 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.7000 0.2830 1.6250 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.2450 0.1820 1.6920 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.5580 -0.9530 0.6860 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.5520 -0.7280 -0.4620 C 0 0
> 0 0 0 0 0 0 0 0 0 0
> 1.2100 -2.0040 -0.4610 O 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4790 -2.6170 -0.6980 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.7050 4.6460 -0.5140 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4180 5.1360 1.1730 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.3040 3.6330 0.8220 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.3730 7.7810 1.3930 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.0420 7.6650 1.5450 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.3330 1.9470 0.0040 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.3310 -0.4740 -0.4150 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.9360 1.8710 0.4260 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.2650 1.0160 -0.3730 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.2400 -0.4910 2.2390 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.3680 1.2710 1.9440 H 0 0 0 0 0 0 0 0
> 0 0 0 0
> -4.7070 1.1170 1.3760 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.5740 -0.0900 2.6950 H 0 0 0 0 0 0 0 0 0 0 0 0
> -5.5810 -0.8670 0.3190 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.3980 -1.9280 1.1470 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.0190 -0.1510 -1.2600 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.2060 -1.6870 -0.8490 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.3400 -3.6850 -0.8680 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.9420 -2.1670 -1.5760 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.1220 -2.4680 0.1690 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 1 22 1 0 0 0 0
> 1 23 1 0 0 0 0
> 1 24 1 0 0 0 0
> 2 3 2 0 0 0 0
> 2 8 1 0 0 0 0
> 3 4 1 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 2 0 0 0 0
> 5 7 1 0 0 0 0
> 7 25 1 0 0 0 0
> 7 26 1 0 0 0
> 0
> 8 9 1 0 0 0 0
> 8 13 2 0 0 0 0
> 9 10 2 0 0 0 0
> 9 27 1 0 0 0 0
> 10 11 1 0 0 0 0
> 10 28 1 0 0 0 0
> 11 12 2 0 0 0 0
> 11 20 1 0 0 0 0
> 12 13 1 0 0 0 0
> 12 14 1 0 0 0 0
> 13 29 1 0 0 0 0
> 14 15 1 0 0 0 0
> 15 16 1 0 0 0 0
> 15 19 1 0 0 0 0
> 15 30 1 0 0 0 0
> 16 17 1 0 0 0 0
> 16 31 1 0 0 0 0
> 16 32 1 0 0 0 0
> 17 18 1 0 0 0 0
> 17 33 1 0 0 0 0
> 17 34 1 0 0 0 0
> 18 19 1 0 0 0 0
> 18 35 1 0 0 0 0
> 18 36 1 0 0 0 0
> 19 37 1 0 0 0 0
> 19 38 1 0 0 0 0
> 20 21 1 0 0 0 0
> 21 39 1 0 0 0 0
> 21 40 1 0 0 0 0
> 21 41 1 0 0 0 0
> M END
> > <name>
> ZINC00000308
>
> $$$$
>
> ------------------------------
>
> _______________________________________________
> Zinc-fans mailing
> list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>
>
> End of Zinc-fans Digest, Vol 37, Issue 1
> ****************************************
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
Walter R.P. Novak, Ph.D.
Postdoctoral Fellow
Rosenstiel Basic Medical Research Center
Brandeis University
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405
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