From jji at cgl.ucsf.edu Wed Jul 2 11:42:27 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 02 Jul 2008 11:42:27 -0700 Subject: [Zinc-fans] download of small subsets of mol2, sdf, and smiles from the results browser page Message-ID: <486BCC13.7000007@cgl.ucsf.edu> Dear ZINC Fans There are a few announcements about ZINC, which can be read on our blog, http://docking.org/. We fixed a problem this morning that was causing downloads of ad hoc subsets of mol2, sdf, and smiles files from the results browser page to either a) run forever or b) suddenly abort after 1-3 minutes. We have just tested on a dozen cases, and it now seems to run reliably quickly - taking up to but no longer than about one minute to assemble and download. A maximum of 2000 molecules can be downloaded in each of these transactions. If you need larger subsets, you can use the "create subset" button to do this. John UCSF ZINC Team From elite158 at gmail.com Fri Jul 4 21:28:35 2008 From: elite158 at gmail.com (elite 158) Date: Sat, 5 Jul 2008 09:58:35 +0530 Subject: [Zinc-fans] "computational Medicinal Chemistry" masters program - requesting suggestions Message-ID: <7811d3d20807042128p45341b79s425127a793fe627a@mail.gmail.com> Dear Zinc Fans and academic stalwarts, Perhaps this isnt a forum to address such issues, but I write to you this mail in high anticipation of receiving your esteemed opinions. I have completed my graduate studies (4 years) in pharmaceutical sciences in India sometime back, and since then working in the same industry (for the past 4 years). My current employment is as a senior research associate in a training company which uses a certain commercial suite of software programs for training participants in 'computational molecular modeling and drug design'. I believe I have hit a dead-end with just a bachelors degree and I presume my career path would be good if I earn a masters degree in a relevant area. With afore mentioned academic history and work experience, I am currently looking for a Masters program, especially in the area of "computational medicinal chemistry". It would also be great to explore any MS-PhD integrated programs (if there are any). As I plan to advance my academic career anywhere overseas, I see that my current financial condition prohibits me from exploring any academic opportunity without proper graduate assistantship. It would be great if anyone could help me suggest a department that would provide me the required financial assistantship either through research or teaching and also would help me add value to the department through my previous work experience. Although I have spent considerable time looking through various University websites and searching using google, I still seek your kind pointers and helpful suggestions. Kindly excuse me if this mail seems to be naive. Regards, elite158 (at) g m a i l . c o m -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080705/b7b2bcca/attachment.html From jji at cgl.ucsf.edu Mon Jul 7 15:46:02 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Mon, 07 Jul 2008 15:46:02 -0700 Subject: [Zinc-fans] "computational Medicinal Chemistry" masters program - requesting suggestions In-Reply-To: <7811d3d20807042128p45341b79s425127a793fe627a@mail.gmail.com> References: <7811d3d20807042128p45341b79s425127a793fe627a@mail.gmail.com> Message-ID: <48729CAA.2050909@cgl.ucsf.edu> Hi Elite 158 I don't think that your question is naive - but it is difficult. I do not have any specific recommendations except - be creative and keep trying. I would prefer that zinc-fans not become a job seekers board, since there are plenty of other venues for that purpose already. John UCSF ZINC Team elite 158 wrote: > > Dear Zinc Fans and academic stalwarts, > > Perhaps this isnt a forum to address such issues, but I write to you > this mail in high anticipation of receiving your esteemed opinions. > > I have completed my graduate studies (4 years) in pharmaceutical > sciences in India sometime back, and since then working in the same > industry (for the past 4 years). > > My current employment is as a senior research associate in a training > company which uses a certain commercial suite of software programs for > training participants in 'computational molecular modeling and drug > design'. > > I believe I have hit a dead-end with just a bachelors degree and I > presume my career path would be good if I earn a masters degree in a > relevant area. With afore mentioned academic history and work > experience, I am currently looking for a Masters program, especially > in the area of "computational medicinal chemistry". It would also be > great to explore any MS-PhD integrated programs (if there are any). > > As I plan to advance my academic career anywhere overseas, I see that > my current financial condition prohibits me from exploring any > academic opportunity without proper graduate assistantship. It would > be great if anyone could help me suggest a department that would > provide me the required financial assistantship either through > research or teaching and also would help me add value to the > department through my previous work experience. > > Although I have spent considerable time looking through various > University websites and searching using google, I still seek your kind > pointers and helpful suggestions. Kindly excuse me if this mail seems > to be naive. > > > Regards, > elite158 (at) g m a i l . c o m > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Jul 9 18:05:29 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 09 Jul 2008 18:05:29 -0700 Subject: [Zinc-fans] Finally, ZINC subsets 3, 6, and 10 are ready for download Message-ID: <48756059.2040504@cgl.ucsf.edu> Dear ZINC-fans: The following subsets are now ready for download: * 3 (drug like) * 6 (all purchasable) * 10 (everything - includes things like pubchem) I have exported them as mol2 and NOT as SDF, since the files are just so darn huge. It is easy to convert mol2 to SDF, using CDK, OEChem/convert.py, OpenBabel, and many other tools. As always, do let us know if anything is not right, and thanks for your patience. If enough people complain about lack of SDF, I'll do something about it. Happy screening! John UCSF ZINC Team From jji at cgl.ucsf.edu Thu Jul 10 16:37:40 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Thu, 10 Jul 2008 16:37:40 -0700 Subject: [Zinc-fans] non-unique ZINC ids in Zinc7 In-Reply-To: <1202726997.9493.14.camel@lsi-08> References: <1202726997.9493.14.camel@lsi-08> Message-ID: <48769D44.6010907@cgl.ucsf.edu> Hi Jens We appreciate this message that you sent us back in February about problems you found in ZINC 7. Since then, a new and I hope much improved version of ZINC, version 8, has appeared. I would be grateful if - should you have time - you would let us know if any of these problems still exist. Best regards John Jens Auer wrote: > 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 > > From shino6483 at hotmail.com Mon Jul 21 23:54:55 2008 From: shino6483 at hotmail.com (=?ks_c_5601-1987?B?vcW/9cjx?=) Date: Tue, 22 Jul 2008 15:54:55 +0900 Subject: [Zinc-fans] To search & browse menu Message-ID: Hello. I used search & browse menu to filter ZINC from some conditions. But I knew that I could only download 2000 molecules only. So, my question is ; are there any rules for selecting these 2000 molecules? Clustering or similarity search methods are used for these molecules? or just random selection? _________________________________________________________________ ? ??? MSN ????, ?? ?? ?????! http://www.msn.co.kr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080722/19cbb8b9/attachment.html From jji at cgl.ucsf.edu Tue Jul 22 08:08:35 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 22 Jul 2008 08:08:35 -0700 Subject: [Zinc-fans] To search & browse menu In-Reply-To: References: Message-ID: <4885F7F3.4010208@cgl.ucsf.edu> Hi - You just get the first 2000 (or so) that match your criteria. The search and browse page in ZINC is designed to let you look up small numbers of molecules reasonably fast, to "look inside" ZINC. If you like what you see, we suggest you download a subset for screening, such as the "lead like" or "fragment like" subsets. There are other kinds of subsets, under the "subsets" pulldown. John UCSF ZINC Team ??? wrote: > Hello. > > I used search & browse menu to filter ZINC from some conditions. > > But I knew that I could only download 2000 molecules only. > > So, my question is ; are there any rules for selecting these 2000 > molecules? > > Clustering or similarity search methods are used for these molecules? > or just random selection? > > > ------------------------------------------------------------------------ > ? ??? ??? ?? ?? ?, ?? ???? ???? ???? ? ? > ?! ? ??? MSN ????! > ------------------------------------------------------------------------ > > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From tomas.malinauskas at gmail.com Tue Jul 22 18:53:39 2008 From: tomas.malinauskas at gmail.com (Tomas Malinauskas) Date: Wed, 23 Jul 2008 02:53:39 +0100 Subject: [Zinc-fans] High-throughput molecular docking using free tools: ZINC 8, AutoDockTools 1.5.2 and Docker 1.0 Message-ID: <70c9a0420807221853x4cbcc215l63f4129fccb3b7ae@mail.gmail.com> Dear All, I would like to share my BASH script (Docker 1.0) for high-throughput molecular docking using ligands from ZINC database and ADT as the molecular docking engine: http://users.ox.ac.uk/~jesu1458/docker/ To illustrate a high-throughput method, docking of the inverse agonist (carazolol)-like ligands to a human beta-2 adrenergic GPCR was performed. Hopefully, Docker 1.0 and the above mentioned page might be useful during tutorials/workshops on virtual screening, ADT, ZINC, etc. Comments are welcome! Best wishes, Tomas From jji at cgl.ucsf.edu Fri Jul 25 11:57:19 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Fri, 25 Jul 2008 11:57:19 -0700 Subject: [Zinc-fans] High-throughput molecular docking using free tools: ZINC 8, AutoDockTools 1.5.2 and Docker 1.0 In-Reply-To: <70c9a0420807221853x4cbcc215l63f4129fccb3b7ae@mail.gmail.com> References: <70c9a0420807221853x4cbcc215l63f4129fccb3b7ae@mail.gmail.com> Message-ID: <488A220F.6000303@cgl.ucsf.edu> Hi Tomas Thank you for sharing your script. I have created an entry on our wiki, http://wiki.compbio.ucsf.edu/wiki/index.php/Docker, which I hope is ok. Please feel free to amend/augement/delete as you see fit. John UCSF ZINC Team Tomas Malinauskas wrote: > Dear All, > > I would like to share my BASH script (Docker 1.0) for high-throughput > molecular docking using ligands from ZINC database and ADT as the > molecular docking engine: > > http://users.ox.ac.uk/~jesu1458/docker/ > > To illustrate a high-throughput method, docking of the inverse agonist > (carazolol)-like ligands to a human beta-2 adrenergic GPCR was > performed. Hopefully, Docker 1.0 and the above mentioned page might be > useful during tutorials/workshops on virtual screening, ADT, ZINC, > etc. > > Comments are welcome! > > Best wishes, > Tomas > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From jpzhou05 at yahoo.com Wed Jul 30 05:31:28 2008 From: jpzhou05 at yahoo.com (jianping zhou) Date: Wed, 30 Jul 2008 05:31:28 -0700 (PDT) Subject: [Zinc-fans] Zinc-fans Digest, Vol 37, Issue 1 In-Reply-To: Message-ID: <384447.47345.qm@web52506.mail.re2.yahoo.com> 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 wrote: From: 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 http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans or, via email, send a message with subject or body 'help' to zinc-fans-request at docking.org You can reach the person managing the list at zinc-fans-owner at docking.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Zinc-fans digest..." 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" Subject: Re: [Zinc-fans] total number of compounds in vendors subset -reg To: rafi A 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" Subject: Re: [Zinc-fans] All-purchasable subset To: "Josmar R. da Rocha" 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 > , > 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 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: doppelte_ids.txt.bz2 Type: application/x-bzip Size: 39034 bytes Desc: not available Url : http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080211/fec82c40/attachment.bin -------------- next part -------------- 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 > 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 > 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 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080730/2375201b/attachment-0001.html From wnovak at brandeis.edu Wed Jul 30 05:42:03 2008 From: wnovak at brandeis.edu (Walter Novak) Date: Wed, 30 Jul 2008 08:42:03 -0400 Subject: [Zinc-fans] Zinc-fans Digest, Vol 37, Issue 1 In-Reply-To: <384447.47345.qm@web52506.mail.re2.yahoo.com> References: <384447.47345.qm@web52506.mail.re2.yahoo.com> Message-ID: <3090B07F-E61A-48ED-A075-D532EC7A37D2@brandeis.edu> 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 > wrote: > From: 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 > > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > or, via email, send a message with subject or body 'help' to > zinc-fans-request at docking.org > > You can reach the person managing the list at > zinc-fans-owner at docking.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Zinc-fans digest..." > > > 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" > Subject: Re: [Zinc-fans] total number of compounds in vendors subset > -reg > To: rafi A > 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" > Subject: Re: [Zinc-fans] All-purchasable subset > To: "Josmar R. da Rocha" > 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 > > > >, > > 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 > 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 > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: doppelte_ids.txt.bz2 > Type: application/x-bzip > Size: 39034 bytes > Desc: not available > Url : > http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080211/fec82c40/attachment.bin > > -------------- next part -------------- > 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 > > > 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 > > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080730/c05bdec7/attachment-0001.html From Florian.Haberl at chemie.uni-erlangen.de Wed Jul 30 06:08:53 2008 From: Florian.Haberl at chemie.uni-erlangen.de (Florian Haberl) Date: Wed, 30 Jul 2008 15:08:53 +0200 Subject: [Zinc-fans] Zinc-fans Digest, Vol 37, Issue 1 In-Reply-To: <384447.47345.qm@web52506.mail.re2.yahoo.com> References: <384447.47345.qm@web52506.mail.re2.yahoo.com> Message-ID: <200807301508.55002.Florian.Haberl@chemie.uni-erlangen.de> Hi, On Wednesday, 30. July 2008, jianping zhou wrote: 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? The compound name is rather generic IUPAC names could be generated with Chemdraw or for example CDK tool kit. It depends on how many molecules you want to parse and if you want commercial tools like MOE. Of course there are also other programs around to work with. Thanks, -jian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) ? 9131 ? 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- From jji at cgl.ucsf.edu Wed Jul 30 09:53:41 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 30 Jul 2008 09:53:41 -0700 Subject: [Zinc-fans] Zinc-fans Digest, Vol 37, Issue 1 In-Reply-To: <384447.47345.qm@web52506.mail.re2.yahoo.com> References: <384447.47345.qm@web52506.mail.re2.yahoo.com> Message-ID: <48909C95.8080805@cgl.ucsf.edu> Hi Jianping 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? > The structure is included in SDF format, and is implicit in the SMILES. The chemical formula is a simple digest of the SMILES. OpenBabel might do this, but you can write one yourself in a few lines of perl or python. IUPAC names can be generated from SMILES by Ogham (OpenEye, eyesopen.com) and other programs. Most compounds in ZINC do not have names other than their IUPAC names, and it is not our remit to keep track of the few that do. Please try ChemDB, http://cdb.ics.uci.edu/CHEM/Web/, and of course PubChem. John UCSF ZINC Team > Thanks, > > -jian > > --- On *Mon, 6/16/08, zinc-fans-request at docking.org > //* wrote: > > From: 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 > > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > or, via email, send a message with subject or body 'help' to > zinc-fans-request at docking.org > > You can reach the person managing the list at > zinc-fans-owner at docking.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Zinc-fans digest..." > > > 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" > Subject: Re: [Zinc-fans] total number of compounds in vendors subset > -reg > To: rafi A > 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" > Subject: Re: [Zinc-fans] All-purchasable subset > To: "Josmar R. da Rocha" > 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 > > > , > > 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 > 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 > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: doppelte_ids.txt.bz2 > Type: application/x-bzip > Size: 39034 bytes > Desc: not available > Url : > http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20080211/fec82c40/attachment.bin > > -------------- next part -------------- > 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 > > > 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 > > > 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 >