[Zinc-fans] Zinc-fans Digest, Vol 37, Issue 1
jianping zhou
jpzhou05 at yahoo.com
Wed Jul 30 05:31:28 PDT 2008
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
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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!
> ------------------------------------------------------------------------
>
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>
------------------------------
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
$$$$
------------------------------
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