From owner-chemistry@ccl.net Wed Nov 23 00:57:00 2005 From: "Eric Scerri scerri() chem.ucla.edu" To: CCL Subject: CCL: latest issue of Hyle now available on Internet Message-Id: <-30044-051123005245-26076-Syki4vbhKk85DmoW2h2ghQ++server.ccl.net> X-Original-From: Eric Scerri Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Tue, 22 Nov 2005 09:50:32 -0800 Mime-Version: 1.0 Sent to CCL by: Eric Scerri [scerri!A!chem.ucla.edu] >>> >>>>HYLE: International Journal for Philosophy of Chemistry >>>>Volume 11 (2005), Number 2 >>>>http://www.hyle.org/journal/issues/11-2/index.html >>>> >>>>Articles: >>>> >>>>Valentin N. Ostrovsky: >>>>"Towards a Philosophy of Approximations in the 'Exact' Sciences" (pp. >>>>101-126) >>>> >>>>Eric R. Scerri: >>>>"Some Aspects of the Metaphysics of Chemistry and the Nature of the >>>>Elements" (pp. 127-145) >>>> >>>>Claus Jacob & Adam Walters: >>>>"Risk and Responsibility in Chemical Research: The Case of Agent >>>>Orange" >>>>(pp. 147-166) >>>> >>>> >>>>Book Reviews: >>>> >>>>Bernadette Bensaude Vincent: >>>>"Marco Beretta (ed.), Lavoisier in Perspective" (pp. 167-168) >>>> >>>>Giovanni Villani: >>>>"Luigi Cerruti, Bella e potente: La chimica del novecento fra scienza >>>>e >>>>societa" (pp. 169-171) >>>> ___________________________________________________________________ From owner-chemistry@ccl.net Wed Nov 23 01:33:00 2005 From: "Yao-Ying Chien chieny[]msu.edu" To: CCL Subject: CCL: CCL and Google Base or Wikipedia, or web-based journals Message-Id: <-30045-051123013155-6977-CE/tPBtwoDgvFNSwERF6Pw#server.ccl.net> X-Original-From: Yao-Ying Chien Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Nov 2005 01:29:59 -0800 MIME-Version: 1.0 Sent to CCL by: Yao-Ying Chien [chieny%msu.edu] Ivan Tubert-Brohman ivan.tubert-brohman{}yale.edu said the following on 2005/11/22 08:48p: >Sent to CCL by: Ivan Tubert-Brohman [ivan.tubert-brohman:yale.edu] >Bill Ross ross^-^cgl.ucsf.edu wrote: > > >>Sent to CCL by: Bill Ross [ross|a|cgl.ucsf.edu] >>I would be very hesitant to cite wikipedia because it will change - >>hopefully for the better - so that in some number of years the >>citation may not make much sense. >> >> > >That's a non-issue. You can always cite the specific version of the page >you are seeing right now, same as any older revision, because all the >revisions are archived. This actually makes it more citable than most >other websites! > > This is becoming interesting. I have been wondering: 1. to publish, we need to pay 2. to read literatures, we need to pay. While many of the research articles are funded by government (= public money), but they can only be accessed by subscribers. I heard from a mathematician that they publish their papers on web-based journals for free with peers review. The readers can add comments on the web-based journals, since many eyes are better than 3 pairs. Many of the Fields Award receivers support the journals. I am interested in hearing discussions in this. For example, is similar trend appearing in computational chemistry? All aspects are appreciated. Thanks, Yao From owner-chemistry@ccl.net Wed Nov 23 05:48:00 2005 From: "Noel O Boyle no228::cam.ac.uk" To: CCL Subject: CCL: Converting CAS names to structures Message-Id: <-30046-051123054606-30479-UGt1podhaaXxBSBoNzkyUQ*server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 23 Nov 2005 10:45:39 +0000 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228,,cam.ac.uk] Dear Kalpana, I think you need to pay Chemical Abstracts some money if you want to look up CAS names in their database. There is no relationship between a CAS name and its structure - it's just an index into the CAS database (in other words, there is no software whether free or not, capable of performing this conversion). You may have some luck with the PubChem database (http://pubchem.ncbi.nlm.nih.gov/), though, which has CAS numbers for most (?) of its entries. These problems with CAS numbers have led IUPAC to develop an Open method for uniquely identified compounds called InCHI, the first version of which was released earlier this year. You may want to read the InCHI FAQ at http://wwmm.ch.cam.ac.uk/inchifaq/, although I am not sure whether this will help with your problem. Regards, Noel On Tue, 2005-11-22 at 22:17 -0500, kalpana krishnaswami kkalpana|,| vsnl.net wrote: > Sent to CCL by: "kalpana krishnaswami" [kkalpana _ vsnl.net] > Hi: > Does anybody know of any 3rd party tools preferably freeware that could convert CAS names to structures? A lot of tools do this with IUPAC names, but I havent been able to find one that converts CAS names. > Regards > Kalpana> > > From owner-chemistry@ccl.net Wed Nov 23 06:29:01 2005 From: "Tim Aitken taitken**accelrys.com" To: CCL Subject: CCL: Converting CAS names to structures Message-Id: <-30047-051123062252-18325-D7u3/xqXYxPsDvoyf8UYrQ/./server.ccl.net> X-Original-From: Tim Aitken Content-Type: multipart/alternative; boundary="=_alternative 003E6673802570C2_=" Date: Wed, 23 Nov 2005 11:21:59 +0000 MIME-Version: 1.0 Sent to CCL by: Tim Aitken [taitken-,-accelrys.com] This is a multipart message in MIME format. --=_alternative 003E6673802570C2_= Content-Type: text/plain; charset="US-ASCII" So on a related point, does anyone know if there is any open source (or other) work going on converting InChIs to IUPAC name? regards, Tim "Noel O Boyle no228::cam.ac.uk" Sent by: owner-chemistry~!~ccl.net 23/11/2005 10:48 Please respond to "CCL Subscribers" To "Aitken, Tim " cc Subject CCL: Converting CAS names to structures Sent to CCL by: "Noel O'Boyle" [no228,,cam.ac.uk] Dear Kalpana, I think you need to pay Chemical Abstracts some money if you want to look up CAS names in their database. There is no relationship between a CAS name and its structure - it's just an index into the CAS database (in other words, there is no software whether free or not, capable of performing this conversion). You may have some luck with the PubChem database (http://pubchem.ncbi.nlm.nih.gov/), though, which has CAS numbers for most (?) of its entries. These problems with CAS numbers have led IUPAC to develop an Open method for uniquely identified compounds called InCHI, the first version of which was released earlier this year. You may want to read the InCHI FAQ at http://wwmm.ch.cam.ac.uk/inchifaq/, although I am not sure whether this will help with your problem. Regards, Noel On Tue, 2005-11-22 at 22:17 -0500, kalpana krishnaswami kkalpana|,| vsnl.net wrote: > Sent to CCL by: "kalpana krishnaswami" [kkalpana _ vsnl.net] > Hi: > Does anybody know of any 3rd party tools preferably freeware that could convert CAS names to structures? A lot of tools do this with IUPAC names, but I havent been able to find one that converts CAS names. > Regards > Kalpanahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/TGkhM+E2!hPSyde0WL76YvwRSSjJWXcIfGLoYN!1VrwuIbHpp0hnBBKDYfZdkMIdYKGoYRR3LQQwSNZvbEbSqQBAi71hzyoKg6Okvhp!2Z!uDHRPEMjp8Y+7inePkgnCOWL6gao1kD806Ux1YILcZmkcxkstysjYLECuy4HyOTuWgRY9ZONl5F4xQmjf1C4lkhKcREPrSoWBlH2VG1hkrFpcRbtHVf+X --=_alternative 003E6673802570C2_= Content-Type: text/html; charset="US-ASCII"
So on a related point, does anyone know if there is any open source (or other) work going on converting InChIs to IUPAC name?

regards,

Tim


"Noel O Boyle no228::cam.ac.uk" <owner-chemistry~!~ccl.net>
Sent by: owner-chemistry~!~ccl.net

23/11/2005 10:48
Please respond to
"CCL Subscribers" <chemistry~!~ccl.net>
To
"Aitken, Tim " <taitken~!~accelrys.com>
cc
Subject
CCL: Converting CAS names to structures





Sent to CCL by: "Noel O'Boyle" [no228,,cam.ac.uk]
Dear Kalpana,

I think you need to pay Chemical Abstracts some money if you want to
look up CAS names in their database. There is no relationship between a
CAS name and its structure - it's just an index into the CAS database
(in other words, there is no software whether free or not, capable of
performing this conversion).

You may have some luck with the PubChem database
(http://pubchem.ncbi.nlm.nih.gov/), though, which has CAS numbers for
most (?) of its entries.

These problems with CAS numbers have led IUPAC to develop an Open method
for uniquely identified compounds called InCHI, the first version of
which was released earlier this year. You may want to read the InCHI FAQ
at http://wwmm.ch.cam.ac.uk/inchifaq/, although I am not sure whether
this will help with your problem.

Regards,
Noel

On Tue, 2005-11-22 at 22:17 -0500, kalpana krishnaswami kkalpana|,|
vsnl.net wrote:
> Sent to CCL by: "kalpana  krishnaswami" [kkalpana _ vsnl.net]
> Hi:
> Does anybody know of any 3rd party tools preferably freeware that could convert CAS names to structures?  A lot of tools do this with IUPAC names, but I havent been able to find one that converts CAS names.
> Regards
> Kalpana>
>
>


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--=_alternative 003E6673802570C2_=-- From owner-chemistry@ccl.net Wed Nov 23 08:31:00 2005 From: "Jonathan Brecher jsb|-|cambridgesoft.com" To: CCL Subject: CCL: Converting CAS names to structures Message-Id: <-30048-051123025037-6392-msACYujLPXHv0HDRzoPQhA~~server.ccl.net> X-Original-From: Jonathan Brecher Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Wed, 23 Nov 2005 00:50:06 -0500 Mime-Version: 1.0 Sent to CCL by: Jonathan Brecher [jsb:+:cambridgesoft.com] >Does anybody know of any 3rd party tools preferably freeware that >could convert CAS names to structures? A lot of tools do this with >IUPAC names, but I havent been able to find one that converts CAS >names. Actually, I don't know of any program that can convert chemical names to structures that *can't* handle CAS names. Both ChemDraw (http://www.cambridgesoft.com) and ACD/Name (http://www.acdlabs.com) definitely can. Of course, either application might fail on any given name, but that would be the exception not the rule. Jonathan Brecher CambridgeSoft Corporation jsb-#-cambridgesoft.com From owner-chemistry@ccl.net Wed Nov 23 09:30:01 2005 From: "Kim Branson kim.branson++gmail.com" To: CCL Subject: CCL: Public HTS screening data Message-Id: <-30049-051123092239-22240-+lF2LP0yYsqgWnez8hTc8Q(~)server.ccl.net> X-Original-From: Kim Branson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Thu, 24 Nov 2005 00:20:45 +1100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Kim Branson [kim.branson%x%gmail.com] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, i'm looking for public HTS screening datasets that I can use to compare docking and scoring methods against. Naturally a structure of the target must be accessible, with the compounds in the screening library. I have the McMasters sets, and I am aware of efforts like chembank, however getting the structures from the database is problematic. If anyone can point me at other sets, or can possibly collaborate i'd be grateful. I'd also like any examples of failed HTS screens, where no "real hits" were found. I think this might prove to be an excellent control for these types of comparisons. cheers kim Dr Kim Branson Peter Doherty Fellow Protein Structure and Function St Vincents Institute for Medical Research 41 Victoria Parade, Fitzroy Victoria 3065, Australia. Phone: +613 9288 2480 Fax: +613 94162 676 Ph +613 9662 7136 kbranson||svi.edu.au kim.branson||gmail.com www.svi.edu.au "Reminds me of the time I went to Africa, someone forgot the corkscrew and we had to live on food and water for days." W.C. Fields -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (Darwin) iD8DBQFDhGyt3QNu8KNs0LgRAlmIAJ9mSmQYupEKDmWNizTD4pntFICtIgCdHfzx D6ipuLHIW7rLzahbNca7fog= =4WQW -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Wed Nov 23 10:05:00 2005 From: "yzhao yzhao,mail.sioc.ac.cn" To: CCL Subject: CCL: seek software about "rule 5" Message-Id: <-30050-051123071945-15370-JBb64Pl/HNn5YSkNgEs4oQ]|[server.ccl.net> X-Original-From: "yzhao" Content-Type: Multipart/Alternative; boundary="------------Boundary-00=_TFOE6RO0000000000000" Date: Wed, 23 Nov 2005 19:40:41 +0800 MIME-Version: 1.0 Sent to CCL by: "yzhao" [yzhao..mail.sioc.ac.cn] --------------Boundary-00=_TFOE6RO0000000000000 Content-Type: Text/Plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Hi, cclers!=0D =0D I'm trying to utilize "rule 5" to filter molecules from a large databas= e. Can anybody tell me where to find some existing program or software that = can do these jobs?=0D Thanks in advance!=0D =0D Steven --------------Boundary-00=_TFOE6RO0000000000000 Content-Type: Text/HTML; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Hi, cclers!
 
  I'm trying to utilize "rule 5" to filter molecules from = a large database. Can anybody tell me where to find some existing pr= ogram or software that can do these jobs?
  Thanks in advance!
 
Steven
--------------Boundary-00=_TFOE6RO0000000000000-- From owner-chemistry@ccl.net Wed Nov 23 10:40:00 2005 From: "Michel Petitjean ptitjean||itodys.jussieu.fr" To: CCL Subject: CCL: molecular modeling freewares for Mac OS X Message-Id: <-30051-051123055938-8494-FTtaKQ2a6xfrUo7w0B13iA|-|server.ccl.net> X-Original-From: Michel Petitjean Date: Wed, 23 Nov 2005 11:59:27 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean],[itodys.jussieu.fr] /* Apologies for unwanted or multiple receipts */ Mac OS X versions of my freewares are now available on my web page: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Please contact me if you encounter problems with them. Thanks. Michel Petitjean, Email: petitjean#,#itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean#,#ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Wed Nov 23 11:15:01 2005 From: "Tamas E. Gunda tgunda2005###puma.unideb.hu" To: CCL Subject: CCL: CCL Converting CAS names to structures Message-Id: <-30052-051123091405-20223-Ovk+MVqsl0l6ZmSugkDIhw!A!server.ccl.net> X-Original-From: "Tamas E. Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-15" Date: Wed, 23 Nov 2005 14:12:33 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas E. Gunda" [tgunda2005]~[puma.unideb.hu] "There is no relationship between a CAS name and its structure - it's just an index into the CAS database" This is wrong. I think that CAS index name and CAS registry numbers have got confused. A CAS name is very related to the structure of the compund, for example: IUPAC name: N,N-dimethyl-1-(4-methyl-1-naphthyl)methanamine CAS index name: 1-naphthalenemethanamine, N,N,4-trimethyl- CAS number: something like 11111-222-33 which has really no relationship with the structure. Dr. Tamas E. Gunda University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry POBox 36 H-4010 Debrecen Hungary e-mail: tgunda2005 *AT* puma.unideb.hu ----- Original Message ----- > From: "Noel O Boyle no228::cam.ac.uk" To: "Gunda, Tamas E " Sent: Wednesday, November 23, 2005 12:02 Subject: CCL: Converting CAS names to structures > Sent to CCL by: "Noel O'Boyle" [no228,,cam.ac.uk] > Dear Kalpana, > > I think you need to pay Chemical Abstracts some money if you want to > look up CAS names in their database. There is no relationship between a > CAS name and its structure - it's just an index into the CAS database > (in other words, there is no software whether free or not, capable of > performing this conversion). > > You may have some luck with the PubChem database > (http://pubchem.ncbi.nlm.nih.gov/), though, which has CAS numbers for > most (?) of its entries. > > These problems with CAS numbers have led IUPAC to develop an Open method > for uniquely identified compounds called InCHI, the first version of > which was released earlier this year. You may want to read the InCHI FAQ > at http://wwmm.ch.cam.ac.uk/inchifaq/, although I am not sure whether > this will help with your problem. > > Regards, > Noel > > On Tue, 2005-11-22 at 22:17 -0500, kalpana krishnaswami kkalpana|,| > vsnl.net wrote: > > Sent to CCL by: "kalpana krishnaswami" [kkalpana _ vsnl.net] > > Hi: > > Does anybody know of any 3rd party tools preferably freeware that could convert CAS names to structures? A lot of tools do this with IUPAC names, but I havent been able to find one that converts CAS names. > > Regards > > Kalpana> > > > From owner-chemistry@ccl.net Wed Nov 23 11:49:01 2005 From: "Michael K. Gilson gilson%a%umbi.umd.edu" To: CCL Subject: CCL: Public HTS screening data Message-Id: <-30053-051123095946-9981-1czBJ5ogQFgt1YxB1h67fQ-$-server.ccl.net> X-Original-From: "Michael K. Gilson" Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Wed, 23 Nov 2005 09:58:14 -0500 MIME-version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson_+_umbi.umd.edu] BindingDB now allows SDfile downloads of compounds and inhibition constants for a given target. I'm not sure if this is exactly what you are after, though, since these are not HTS sets. On the other hand, some targets have hundreds of compounds. You might also want to look at what is available now at PubChem. Regards, Mike Kim Branson kim.branson++gmail.com wrote: >Sent to CCL by: Kim Branson [kim.branson%x%gmail.com] >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > > >Hi all, > >i'm looking for public HTS screening datasets that I can use to compare >docking and scoring methods against. Naturally a structure of the >target must be accessible, with the compounds in the screening >library. I have the McMasters sets, and I am aware of efforts like >chembank, however getting the structures from the database is >problematic. If anyone can point me at other sets, or can possibly >collaborate i'd be grateful. > >I'd also like any examples of failed HTS screens, where no "real hits" >were found. I think this might prove to be an excellent control for >these types of comparisons. > >cheers > >kim > >Dr Kim Branson >Peter Doherty Fellow >Protein Structure and Function >St Vincents Institute for Medical Research >41 Victoria Parade, Fitzroy >Victoria 3065, Australia. >Phone: +613 9288 2480 >Fax: +613 94162 676 >Ph +613 9662 7136 >kbranson=-=svi.edu.au >kim.branson=-=gmail.com >www.svi.edu.au > > "Reminds me of the time I went to Africa, someone forgot the corkscrew >and we had to live on food and water for days." >W.C. Fields > > >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.2.4 (Darwin) > >iD8DBQFDhGyt3QNu8KNs0LgRAlmIAJ9mSmQYupEKDmWNizTD4pntFICtIgCdHfzx >D6ipuLHIW7rLzahbNca7fog= >=4WQW >-----END PGP SIGNATURE-----> > > > > -- Michael K. Gilson, M.D., Ph.D. CARB Fellow and Professor Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Voice: 240-314-6217 Fax: 240-314-6255 gilsonumbi.umd.edu From owner-chemistry@ccl.net Wed Nov 23 12:26:00 2005 From: "Jim Kress ccl_nospam^^kressworks.com" To: CCL Subject: CCL: CCL and Google Base or Wikipedia, or web-based journals Message-Id: <-30054-051123122230-4262-LNCNgr0bDlYURJXp41Dztw###server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 Nov 2005 12:22:14 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam-,-kressworks.com] > While many of the research articles are funded by government > (= public money), but they can only be accessed by = money of individual citizens taken by government force depriving them of the ability to meet their own needs. HOWEVER, using Wikipedia as a publishing resource for technical journals might be an interesting idea. It would provide a common point of access, a mechanism for controlled annotation and review with proper attribution to the reviewer(s) and annotator(s). It could also provide a discussion board for comments and observations. Jim > -----Original Message----- > From: Yao-Ying Chien chieny[]msu.edu [mailto:owner-chemistry]-[ccl.net] > Sent: Wednesday, November 23, 2005 2:37 AM > To: Kress, Jim > Subject: CCL: CCL and Google Base or Wikipedia, or web-based journals > > Sent to CCL by: Yao-Ying Chien [chieny%msu.edu] Ivan > Tubert-Brohman ivan.tubert-brohman{}yale.edu said the following on > 2005/11/22 08:48p: > > >Sent to CCL by: Ivan Tubert-Brohman > [ivan.tubert-brohman:yale.edu] Bill > >Ross ross^-^cgl.ucsf.edu wrote: > > > > > >>Sent to CCL by: Bill Ross [ross|a|cgl.ucsf.edu] I would be very > >>hesitant to cite wikipedia because it will change - > hopefully for the > >>better - so that in some number of years the citation may not make > >>much sense. > >> > >> > > > >That's a non-issue. You can always cite the specific version of the > >page you are seeing right now, same as any older revision, > because all > >the revisions are archived. This actually makes it more citable than > >most other websites! > > > > > This is becoming interesting. I have been wondering: > 1. to publish, we need to pay > 2. to read literatures, we need to pay. > > While many of the research articles are funded by government > (= public money), but they can only be accessed by > subscribers. I heard from a mathematician that they publish > their papers on web-based journals for free with peers > review. The readers can add comments on the web-based > journals, since many eyes are better than 3 pairs. Many of > the Fields Award receivers support the journals. I am > interested in hearing discussions in this. For example, is > similar trend appearing in computational chemistry? All > aspects are appreciated. > > Thanks, > Yao > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the ]-[ sign. You can also look up the X-Original-From: line > in the mail header.> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Wed Nov 23 13:01:01 2005 From: "Greg Landrum Landrum-*-RationalDiscovery.com" To: CCL Subject: CCL: Public HTS screening data Message-Id: <-30055-051123123636-16859-8uvwtQyoolytcVgiM9JNvQ[A]server.ccl.net> X-Original-From: Greg Landrum Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Nov 2005 09:36:26 -0800 MIME-Version: 1.0 Sent to CCL by: Greg Landrum [Landrum!^!RationalDiscovery.com] Kim Branson kim.branson++gmail.com wrote: > > i'm looking for public HTS screening datasets that I can use to compare > docking and scoring methods against. Naturally a structure of the > target must be accessible, with the compounds in the screening > library. I have the McMasters sets, and I am aware of efforts like > chembank, however getting the structures from the database is > problematic. If anyone can point me at other sets, or can possibly > collaborate i'd be grateful. > Though it's not exactly HTS data, a large quantity of data about CDK2 ligands is available in the supplementary material associated with this paper: Bradley, E. K.; Miller, J. L.; Saiah, E.; Grootenhuis, P. D. Informative library design as an efficient strategy to identify and optimize leads: application to cyclin-dependent kinase 2 antagonists. J Med Chem 2003, 46, 4360-4364. http://dx.doi.org/10.1021/jm020472j The authors screened ~16K compounds for CDK2 activity and report all the results. -greg From owner-chemistry@ccl.net Wed Nov 23 14:05:01 2005 From: "Wolf-D. Ihlenfeldt wdi!A!xemistry.com" To: CCL Subject: CCL: Public HTS screening data Message-Id: <-30056-051123134146-24622-iNIp5ioffPjwO3lCiVzB6Q~!~server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 Nov 2005 13:04:39 -0500 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi%a%xemistry.com] I suggest you look at PubChem (pubchem.ncbi.nlm.nih.gov). W. D. Ihlenfeldt Xemistry GmbH wdi[]xemistry.com > -----Original Message----- > From: owner-chemistry[]ccl.net [mailto:owner-chemistry[]ccl.net] > Sent: Wednesday, November 23, 2005 9:38 AM > To: Ihlenfeldt, W.d. > Subject: CCL: Public HTS screening data > > > Sent to CCL by: Kim Branson [kim.branson%x%gmail.com] > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hi all, > > i'm looking for public HTS screening datasets that I can use > to compare > docking and scoring methods against. Naturally a structure of the > target must be accessible, with the compounds in the screening > library. I have the McMasters sets, and I am aware of efforts like > chembank, however getting the structures from the database is > problematic. If anyone can point me at other sets, or can possibly > collaborate i'd be grateful. > > I'd also like any examples of failed HTS screens, where no > "real hits" > were found. I think this might prove to be an excellent control for > these types of comparisons. > > cheers > > kim > > Dr Kim Branson > Peter Doherty Fellow > Protein Structure and Function > St Vincents Institute for Medical Research > 41 Victoria Parade, Fitzroy > Victoria 3065, Australia. > Phone: +613 9288 2480 > Fax: +613 94162 676 > Ph +613 9662 7136 > kbranson=-=svi.edu.au > kim.branson=-=gmail.com > www.svi.edu.au > > "Reminds me of the time I went to Africa, someone forgot > the corkscrew > and we had to live on food and water for days." > W.C. Fields > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.2.4 (Darwin) > > iD8DBQFDhGyt3QNu8KNs0LgRAlmIAJ9mSmQYupEKDmWNizTD4pntFICtIgCdHfzx > D6ipuLHIW7rLzahbNca7fog= > =4WQW > -----END PGP SIGNATURE----- > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the [] sign. You can also look up the X-Original-From: line > in the mail header.> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From owner-chemistry@ccl.net Wed Nov 23 14:40:02 2005 From: "Loan Huynh huynhkl2000_+_yahoo.ca" To: CCL Subject: CCL: seek software about "rule 5" Message-Id: <-30057-051123135354-25729-cmSI1p9KDEyd+L43+lqKrA]*[server.ccl.net> X-Original-From: Loan Huynh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-390175027-1132772027=:96000" Date: Wed, 23 Nov 2005 13:53:47 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000:-:yahoo.ca] --0-390175027-1132772027=:96000 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Steven, The CAChe software can do this. "yzhao yzhao,mail.sioc.ac.cn" wrote: Sent to CCL by: "yzhao" [yzhao..mail.sioc.ac.cn] --------------Boundary-00=_TFOE6RO0000000000000 Content-Type: Text/Plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Hi, cclers!=0D =0D I'm trying to utilize "rule 5" to filter molecules from a large databas= e. Can anybody tell me where to find some existing program or software that = can do these jobs?=0D Thanks in advance!=0D =0D Steven --------------Boundary-00=_TFOE6RO0000000000000 Content-Type: Text/HTML; charset="gb2312" Content-Transfer-Encoding: quoted-printable FLAVOR00-NONE-0000-0000-000000000000 4.0 ; 10px 10px; FONT-FAMILY: Arial" bgColor=3D#ffffff background=3D"" scroll=3D= yes ORGYPOS=3D"0"> %" border=3D0> AMILY: Arial" width=3D"100%"> Hi, cclers! I'm trying to utilize "rule 5" to filter molecules from = a large database. Can anybody tell me where to find some existing pr= ogram or software that can do these jobs? Thanks in advance! Steven ABLE> --------------Boundary-00=_TFOE6RO0000000000000--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Find your next car at Yahoo! Canada Autos --0-390175027-1132772027=:96000 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi Steven,
The CAChe software can do this.

"yzhao yzhao,mail.sioc.ac.cn" <owner-chemistry-$-ccl.net> wrote:
Sent to CCL by: "yzhao" [yzhao..mail.sioc.ac.cn]

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Hi, cclers!=0D
=0D
I'm trying to utilize "rule 5" to filter molecules from a large databas=
e.
Can anybody tell me where to find some existing program or software that =
can
do these jobs?=0D
Thanks in advance!=0D
=0D
Steven
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Find your next car at Yahoo! Canada Autos --0-390175027-1132772027=:96000-- From owner-chemistry@ccl.net Wed Nov 23 17:11:01 2005 From: "Michael K. Gilson gilson###umbi.umd.edu" To: CCL Subject: CCL: BindingDB down... Message-Id: <-30058-051123170427-21688-10Y6I079CvkGPTXbjlLJuw a server.ccl.net> X-Original-From: "Michael K. Gilson" Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Wed, 23 Nov 2005 17:02:48 -0500 MIME-version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson(_)umbi.umd.edu] Naturally as soon as I mentioned BindingDB on CCL this time, our site went down! My apologies to folks who are trying to access it. I will try to have this remedied soon, but I'm not sure it will be back before Monday... Have a good Thanksgiving, Mike
AMILY: Arial" width=3D"100%">
Hi, cclers!


  I'm trying to utilize "rule 5" to filter molecules from =
a large database. Can anybody tell me where to find some existing pr=
ogram or software that can do these jobs?

  Thanks in advance!

 

Steven






ABLE>

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