From chemistry-request@server.ccl.net Tue Aug 8 09:56:05 2000 Received: from GOOFY1.UNI-MUENSTER.DE (postfix@GOOFY1.UNI-MUENSTER.DE [128.176.220.205]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31212 for ; Tue, 8 Aug 2000 09:56:04 -0400 Received: from GOOFY1 (localhost.uni-muenster.de [127.0.0.1]) by GOOFY1.UNI-MUENSTER.DE (Postfix) with SMTP id D9C35757CF for ; Tue, 8 Aug 2000 15:58:24 +0200 (CEST) From: Stefan Grimme Organization: Universitaet Muenster, Organisch-Chemisches Institut To: CHEMISTRY@ccl.net Subject: CCL:group electronegativities Date: Tue, 8 Aug 2000 15:53:01 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <00080815581901.29742@GOOFY1> Content-Transfer-Encoding: 8bit Dear CCL, does anybody know about recent (last 10 years) theoretical approaches for calculating group electronegativities? Thanks in advance. Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes@uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ _________________________________________________________ From chemistry-request@server.ccl.net Tue Aug 8 03:02:54 2000 Received: from fortytwo.csc.cuhk.edu.hk (root@fortytwo.csc.cuhk.edu.hk [137.189.6.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA28667 for ; Tue, 8 Aug 2000 03:02:53 -0400 Received: from mailserv.cuhk.edu.hk (IDENT:lard@[137.189.50.96]) by fortytwo.csc.cuhk.edu.hk (8.9.3/8.9.3) with ESMTP id PAA26668 for ; Tue, 8 Aug 2000 15:02:43 +0800 (HKT) Sender: lard@mailserv.cuhk.edu.hk Message-ID: <398FAF15.27F64E30@mailserv.cuhk.edu.hk> Date: Tue, 08 Aug 2000 14:56:22 +0800 From: Lawrence Tsang Organization: AUC X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Autodock of hormones with receptor. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am using Autodock to dock human growth hormone 3hhra to one of it's receptor in 3hhr (receptor 1 3hhrb). But after running autotors (for 3 hr! becoz 3xxx lines in *.bnd file), it said "unable to attach all piece of data in bond file". the 3d structure of 3hhra itself have "gap" due to disorder, I am looking forward to hear hints about if this error is due to too large of ligand or due to "disorder". Thank you. Best wishes. Lawrence. Dept of Biochemistry. Chinese University of Hong Kong. From chemistry-request@server.ccl.net Tue Aug 8 07:23:52 2000 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA30689 for ; Tue, 8 Aug 2000 07:23:51 -0400 Received: from pat.biochem.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 8 Aug 2000 12:23:06 +0100 Received: from bsmir18 (bsmir18 [128.40.46.21]) by pat.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id MAA02769 for ; Tue, 8 Aug 2000 12:23:18 +0100 Date: Tue, 8 Aug 2000 12:23:17 +0100 (BST) From: Irilenia Nobeli X-Sender: nobeli@bsmir18 Reply-To: Irilenia Nobeli To: Computational Chemistry List Subject: Summary of replies: software for databases of chemical info Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers I have received a wide range of responses to my question on software (free and commercial) for databases of chemical structures. I was only going to do a summary but I thought it best to let everybody read the original answers so they can make up their own minds. However, for those who don't want to go through the e-mails, and for what it's worth, here is my conclusion (I must stress that we have not made a decision yet as we are still waiting for quotations from a few companies). --- There does not seem to be any FREE software around that will allow either the creation of a database of chemical structures (and of course tools to retrieve data and do substructure/similarity searches) or an interface to a standard relational database that will allow the handling of chemical structures. If I am wrong about this one, please let me know! --- There are a few commercial products around that promise they can do just the job. Most of them are guaranteed to set you back a few thousand dollars, although allow me to praise ChemAxon for their policy regarding the pricing of their product JChem. For a (hopefully near-complete) list: JChem from ChemAxon ISIS from MDL UNITY from Tripos MOE from the Chemical Computing Group RS3 from Oxford Molecular ACCORD from Synopsys ChemFolder from ACDlabs (if I missed any, I'm sure someone will let me know!) --- I had recommendations (NOT FROM THE DEVELOPERS THEMSELVES!) for JChem, RS3, ISIS and MOE. I would also like to point out that ChemFolder cannot be interfaced to Oracle but its price is a fraction of most other commercial software. Finally, before I attach the original answers let me thank once again all those who helped with their e-mails. >From dark grey London, Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk tel. 020 7679 2171 fax. 020 7679 7193 >>> The greatest proof of the existence of intelligent life outside Earth is that they haven't contacted us yet. <<<< >>>>>>>>>>>>>>>>>>>> EDITED ANSWERS <<<<<<<<<<<<<<<<<<<<<<<<< Date: Wed, 02 Aug 2000 14:47:27 +0100 From: Herbert Fruchtl Hi Irilenia, Knowing next to nothing about databases myself, here's a list of free database applications for Linux: http://metalab.unc.edu/pub/Linux/apps/database/!INDEX.html I think the most widely used one is SQL, and in the www directory from this page there's a CGI (that's a scripting language for web sites) front-end. No idea if it's any good, or if it's useful for the type of database you have in mind. --------------------------------------------------------------------- Date: Wed, 2 Aug 2000 11:00:16 -0400 From: Carlos Faerman Irilenia, There are two major players that utilize ORACLE to build such a database: MDL and Oxford Molecular Group, UK. The former calls it ChemBio4Oracle whereas the latter calls it RS3. I am not aware of freeware to do this. You may also check Specs/BioSpecs in Holland who have a Web interface that customers can use to purchase compounds, naturally linked to their database which I believe is RS3-based. Carlos ---------------------------------------------------------------------- Date: Wed, 2 Aug 2000 16:07:17 +0100 From: David S Coombes [...] I don't really have a reply to your problem but if you want to have a web interface i think perl/cgi scripts can be very useful. What sort of information would your database contain? -------------------------------------------------------------------------- Date: Wed, 02 Aug 2000 11:29:11 -0400 From: "Michael K. Gilson" Hi, We are using JChem and are quite happy with it so far. See "substructure search" in http://www.bindingdb.org good luck, Mike --------------------------------------------------------------------------- Date: Wed, 2 Aug 2000 16:36:00 +0100 From: Rob Williams Hi, Just for the record, you missed Oxford Molecular from your list of commercial suppliers. We are the main suppliers of Oracle based chemistry databases. We have had a product, RS3 (RS-cubed), on the market for some years now that allows structures to be managed, searched and retrieved directly in Oracle. It also supports combined queries across chemical structure and any other data you might have stored in Oracle. It is a full informatics solution with the emphasis on information sharing between co-workers. We have a web toolkit in final QA before release at the end of this month. This allows you to put together your end web applications very quickly using JavaServer Pages (JSP). I mention this because if you do go for a commercial solution then we really do have the best product offering. Other vendors may have data cartridges for Oracle that can perform a substructure query but RS3 is a full database application on top of this sort of technology. You can get more information from our web site at http://www.oxmol.com, and on the new web toolkit specifically at http://www.oxmol.com/software/rs3iab. Hope this is useful for you. Best regards, Rob ------------------------------------------------------------------------ Date: Wed, 2 Aug 2000 16:33:41 +0100 From: "George, Ashley" Hi, I'm really interested in your note and the types of things you are trying to do. Is it possible to explain what you are finally going for? Substructure searching, reaction searching, just text based searching? Hopefully speak to yo usoon Cheers Ashley Dr Ashley George UK Group Leader Chemoinformatics GlaxoWellcome Medicine Research Centre Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK Direct Tel. +44(0)1438-764183 Direct Fax. +44(0)1438-764918 email. ayg8615@glaxowellcome.co.uk --------------------------------------------------------------------- Date: Wed, 02 Aug 2000 17:15:50 +0100 From: Mark Forster Dear Irilenia Mark here. I saw your question on the CCL, and thought I could add my $0.02 worth. What is the hardware/OS on which you want to run the database - is it exclusively SGI. For an alternative I would suggest PostgresSQL or MySQL on a PC/Linux. I have Suse Linux 6.3 and these are included in the box, although I dont have an application that uses them (yet). The web interface would only need to be HTML/CGI/Perl and the development effort here is quite low, there are also many examples around. [...] Mark F ------------------------------------------------------------------------ Date: Thu, 3 Aug 2000 09:26:10 +1000 From: "Dr. Dave Winkler" I would like to see a summary of responses please, Irilenia. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia ------------------------------------------------------------------------- Date: Wed, 02 Aug 2000 21:59:20 +0200 From: Thomas Strassner Dear Irene, though I can not give you any hints besides what you mentioned I would be very interested in a summary of replies. Please post it to CCL, I think many people will be interested !! Yours sincerely Thomas Strassner --------------------------------------------------------------------------- Date: Thu, 03 Aug 2000 13:12:23 +0200 From: michael braunschweig hi irilenia, we tested the mdl database last year. the text as the structure search are quite fast (if you have a server woth lot of memory - 4 * rs64-ii 262 mhz / 8mb L2 Cache, 6 bg memory). in my opinion the substructure search is a very good feature. michael braunschweig department of chemistry university of dortmund germany --------------------------------------------------------------------------- Date: Thu, 3 Aug 2000 14:34:41 -0400 From: Gavin Shear Dear Irilenia, ACD/Chemfolder will suit your purpose. Please see www.acdlabs.com/downloads for a free trial version. Although the database is not currently Oracle based, academic prices are very reasonable, and multiple user database searching etc. is supported. Hope this helps, Gavin Shear ------------------------------------------------------------------------- Date: Thu, 3 Aug 2000 17:59:06 -0400 (EDT) From: Suzanne Sirois Dear Irilenia, I have developed a software in JAVA that can access any database. MS-ACCESS, MySQL, Oracle. What is important to know is what exactly you want to do with the DB. Molecular Modeling, HTS, data mining, etc. One software that has all of the above is MOE from Chemical Computing Group. It is not free but much more cheaper than other commercial software. Goud Luck, Suzanne Sirois Pharmaceutical Chemistry Business development officer --------------------------------------------------------------------------- Date: Fri, 04 Aug 2000 00:57:35 +0200 From: Ferenc Csizmadia Hi Irilenia, JChem suits your requirements: - allows you to access, search and retrieve data, - structures may be stored in Oracle (or other SQL-based relational database system) - supports web access - used by academic institutions - affordable Since the software is in Java, you may use it under any OS-s (Linux, Win32, Sun, SGI, ....) Please check out http://www.jchem.com, where you can see the software working (you can also download it for evaluation). Regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com ------------------------------------------------------------------------ Date: Fri, 04 Aug 2000 07:44:32 -0400 From: Anthony Arvanites Dear Irilenia Ferenc's software JChem would probably best fit your needs and its practically free. I highly recommend the JChem software. If you decide to go with commercial software, your best choice would be MDL. MDL will give you a considerable licensing discount because you are in a academic setting. Good luck Tony ------------------------------------------------------------------------- Date: Fri, 4 Aug 2000 09:59:12 -0400 (EDT) From: Suzanne Sirois Dear Irilenia, I have experience with MOE in the past and what you are looking for is in it. Also, they have academic price which are very good! Trust me it is a good program. Please contact Bill Hayden at 514-393-1005 or 514 944 5953 hayden@chemcomp.com You can mention that I refer you to him. Suzanne Sirois, Ph.D. Pharmaceutical Chemistry business development officer CERCA ------------------------------------------------------------------------ Date: Mon, 07 Aug 2000 14:02:55 EDT From: Douglas Smith` Irilenia: You did not mention RS3 from Oxford Molecular in your mail to CCL. It has been an Oracle technology for chemistry for far longer than any of the other commercial packages you mentioned. If you would like, I will have a sales person call on you or send you additional information about the product and academic pricing. Doug Smith Product Manager, Decision Support Software OMG dsmith@oxmol.com 410-527-4571 From chemistry-request@server.ccl.net Tue Aug 8 11:32:02 2000 Received: from mail.virginia.edu (mail.Virginia.EDU [128.143.2.9]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA31699 for ; Tue, 8 Aug 2000 11:32:02 -0400 Received: from unix.mail.virginia.edu by mail.virginia.edu id aa21764; 8 Aug 2000 11:31 EDT Received: from patch2 (bootp-44-24.bootp.Virginia.EDU [128.143.44.24]) by unix.mail.Virginia.EDU (8.9.3/8.9.3) with SMTP id LAA73290 for ; Tue, 8 Aug 2000 11:31:48 -0400 Message-Id: <3.0.6.32.20000808110946.0084cb80@unix.mail.virginia.edu> X-Sender: ps2t@unix.mail.virginia.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 08 Aug 2000 11:09:46 -0400 To: chemistry@ccl.net From: Pornthep Sompornpisut Subject: optimization method for multisubunit protein model Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues, Does any body know an appropriate methodology or strategy to perform energy minimization of the protein model system containing identical multisubunit (tetra, penta or hexameric) arrangement? Since the optimization using different methods (Powell, SD, CG) produces unsymmetrically conformational changes. My point is that the same conformational change should take place every subunit, not change only one or two subunits greater than the remaining subunits. Any comments are appreciate? Thank you. Thep ======================================================================= Pornthep Sompornpisut, Ph.D Postdoctoral Fellow Molecular Physiology & Biological Physics University of Virginia 1300 Jefferson Park Ave Charlottesville VA 22906 Tel: 804-924-5473 Fax: 804-982-1616 Email:ps2t@virginia.edu ======================================================================= From chemistry-request@server.ccl.net Tue Aug 8 15:17:17 2000 Received: from mr2.wpafb.af.mil (mr2o.wpafb.af.mil [129.48.104.214]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00513 for ; Tue, 8 Aug 2000 15:17:17 -0400 Received: from fszhtv02.wpafb.af.mil (fszhtv02.wpafb.af.mil [129.48.26.234]) by mr2.wpafb.af.mil (8.10.2/8.10.2) with ESMTP id e78JHJF12896; Tue, 8 Aug 2000 15:17:19 -0400 (EDT) Received: by fszhtv02.wpafb.af.mil with Internet Mail Service (5.5.2650.21) id ; Tue, 8 Aug 2000 15:17:18 -0400 Message-ID: <45EE82EFB176D311815F0000F8CD23546C9C1E@fszhtv48.ml.wpafb.af.mil> From: Nguyen Kiet A Contr AFRL/MLPJ To: "'chemistry@ccl.net'" Cc: "'help@gaussian.com'" Subject: Strange CI Coefs in G98 Date: Tue, 8 Aug 2000 15:15:43 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="windows-1252" I have found that the TDDFT coefs in G98 were different for the same system running on different machines. Mike Frisch did point out that the mixing of excitations to the pair of degenerate excited states is arbitrary and may be different on different machines. Indeed, I found that sums of the square of the TD-DFT coefs of different machines for a give state are about the same. However, neither Frisch nor help@gaussian.com responded to the question of how G98 (not) normalizes the excited wavefuntions (RPA, CIS, and TDDFT). I a simple cases (H2O and H2), the sum of the square of ALL CIS ci coefs in for the first excite state is not even close to 1. In contrast, TDDFT coefs printed out by G98 are greater than 1 for free-base tetraphenylporphyrin. Excited State 1: ?Spin -A2 0.3133 eV 3957.70 nm f=0.0000 169A ->173A 0.10119 171A ->172A 1.10520 This state for optimization and/or second-order correction. Total Energy, E(RPA) = -2138.68813447 Copying the excited state density for this state as the 1-particle RhoCI densit y. Excited State 2: ?Spin -A2 0.5963 eV 2079.13 nm f=0.0000 169B ->170B 1.02651 Should the sum of the square of the TD-DFT coefs = 1, in addition to the biorthormal, = 1? Also a note of caution for the symmetry labels in G98, toward the end of the excited state calculations, the program calls LASSW to determine the largest non-zero coefs. and assign multiplicity even though it is an input value and calculated at then end of the scf cycle ( value the triplet case above is very close to 2.0). The multiplicity is assigned based on the beta and alpha coefs. When the alpha and beta coefs differ significantly for a number of orbital in the unrestricted calculations, the program (LASSW) cannot determine the multiplicity and prints ?Spin. The electronic symmetries, however, are assigned assuming a totally symmetric ground state that are often not the case. So the electronic symmetries (-A2) assigned by the program for the case above are WRONG. Have anyone encounter these problems? I have not looked at other parts of CI/TDDFT codes. I appreciate any insight for anyone who have decoded the CI/TDDFT coefs . Kiet Nguyen AFRL/Laser Hardened Materials Branch Wright-Patterson AFB, OH 45433 FAX (937) 255-1128 From chemistry-request@server.ccl.net Tue Aug 8 16:01:05 2000 Received: from fortytwo.csc.cuhk.edu.hk (root@fortytwo.csc.cuhk.edu.hk [137.189.6.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA00702 for ; Tue, 8 Aug 2000 16:01:04 -0400 Received: from cuhk.edu.hk (lard@h237103.resnet.cuhk.edu.hk [137.189.237.103]) by fortytwo.csc.cuhk.edu.hk (8.9.3/8.9.3) with ESMTP id EAA01938 for ; Wed, 9 Aug 2000 04:01:03 +0800 (HKT) Sender: lard@mailserv.cuhk.edu.hk Message-ID: <399067DC.3729CB70@cuhk.edu.hk> Date: Wed, 09 Aug 2000 04:04:44 +0800 From: Lawrence Tsang Organization: AUC X-Mailer: Mozilla 4.61 [zh_TW.Big5] (X11; I; Linux 2.2.15-3 i586) X-Accept-Language: en MIME-Version: 1.0 To: "'chemistry@ccl.net'" Subject: autodock: what to do if some limbs not attached in autotors? Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit Hello, I am trying to dock hormone to receptor, but in using autotors to prepare the hormone, it says "unable to attach all pieces of bond data", i saw in source code means treecount>treenum, and what can I do now? (The hormone have disulphide bond, will that the problem?) Looking forward to hearing any hints. Thank you. Best wishes, Lawrence Tsang. From chemistry-request@server.ccl.net Tue Aug 8 18:15:46 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA01197 for ; Tue, 8 Aug 2000 18:15:42 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id PAA03598; Tue, 8 Aug 2000 15:11:40 -0700 (PDT) Received: from dial11.msi.com(146.202.9.111) by mailhost.msi.com via smap (V2.0) id xma003594; Tue, 8 Aug 00 15:11:13 -0700 Message-Id: <4.2.0.58.20000807233237.00d805b0@146.202.6.217> X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Mon, 07 Aug 2000 23:55:37 -0500 To: Joe M Leonard , chemistry@ccl.net From: "Osman F. Guner" Subject: Re: CCL:Seeking information in two areas... In-Reply-To: <200008032306.TAA14972@world.std.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_438059==_.ALT" --=====================_438059==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable HipHop pharmacophores are prioritized based on how well the training set=20 fits onto a pharmacophore. The following two papers may provide more=20 information. Greene, J.; Kahn, S.; Savoj, H.; Sprague, P.; Teig, S. "Chemical=20 Function Queries for 3D Database Search", J. Chem. Inf. Comput. Sci., 1994,= =20 34, 1297-1308. Clement, O. O.; Trope-Mehl, A. "HipHop: Pharmacophores based on=20 multiple common-feature alignments," in Pharmacophore Perception,=20 Development, and Use in Drug Design, G=FCner, O. F. Ed., Int. Univ. Line,=20 2000, La Jolla, 69-83. I have been proposing follow up database searching and evaluation of the=20 search results to validate pharmacophores. Analysis of several metrics are= =20 published, together with the GH-score which is a weighted linear=20 combination of two factors that address the selectivity as well as coverage= =20 of pharmacophores at: G=FCner, O. F.; Henry, D. R. "Metric for analyzing hit lists and=20 pharmacophores," in Pharmacophore Perception, Development, and Use in Drug= =20 Design, G=FCner, O. F. Ed., Int. Univ. Line, 2000, La Jolla, 191-211. Most of the above are covered in some details in "the Pharmacophore=20 book". Go to www.amazon.com or www.barnesandnoble.com and search for the=20 keyword "pharmacophore." A detailed review of the book (written by Lisa=20 Balbes) can be found at ChemWeb=20 http://www.chemweb.com/alchem/2000/books/bk_000728_osman.html As far as conformational diversity, see the following three papers and=20 references within: Smellie, A.; Teig, S. L.; Towbin, P. "Poling: Promoting Conformational=20 Coverage", J. Comp. Chem., 1995, 16, 171-187. Smellie, A.; Kahn, S. D.; Teig, S. "An Analysis of Conformational Coverage= =20 1. Validation and Estimation of Coverage", J. Chem. Inf. Comput. Sci.,=20 1995, 35, 285-294. Smellie, A.; Kahn, S. D.; Teig, S. "An Analysis of Conformational Coverage= =20 2. Applications of Conformational Models", J. Chem. Inf. Comput. Sci.,=20 1995, 35, 295-304. Hope this helps a bit. Thx...osman At 07:06 PM 8/3/00 -0400, Joe M Leonard wrote: >Folks, > >When I was at ACS SF in 1997, several of us discussed whether >there were any published methods to score pharmacophores without >having to do the search(es) and compare the results. The lunch- >consensus was that nobody had done this, and that it was an >interesting area... Therefore, were we wrong in 1997, or has >there been work done since then that I should be aware of? > > >Also, I am interested in investigating conformational diversity, >and seek similar information. I've got some ideas, but hate to >reinvent wheels... Are there particular papers I should run >down, or people I should talk to? > >Pointers, citations, whatever appreciated! If the responses >are good, I'll summarize... > >Joe > >P.S. If people want to talk about this, I'll be at EuroQSAR >(and at ACS for a short while). > > >-=3D This is automatically added to each message by mailing script =3D- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To=20 >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net= 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan:= jkl@ccl.net > > > > --- Osman F. G=FCner, Ph.D. Director, Lead Identification & Optimization Molecular Simulations Inc. (858) 799-5341 osman@msi.com http://www.msi.com=20 --=====================_438059==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable HipHop pharmacophores are prioritized based on how well the training set fits onto a pharmacophore.  The following two papers may provide more information.

       &nbs= p;Greene, J.; Kahn, S.; Savoj, H.; Sprague, P.; Teig, S. "Chemical Function Queries for 3D Database Search", J. Chem. Inf. Comput. Sci., 1994, 34, 1297-1308.

        Clement, O. O.; Trope-Mehl, A. "HipHop: Pharmacophores based on multiple common-feature alignments," in Pharmacophore Perception, Development, and Use in Drug Design, G=FCner, O. F. Ed., Int. Univ. Line, 2000, La Jolla, 69-83.

I have been proposing follow up database searching and evaluation of the search results to validate pharmacophores.  Analysis of several metrics are published, together with the GH-score which is a weighted linear combination of two factors that address the selectivity as well as coverage of pharmacophores at:

G=FCner, O. F.; Henry, D. R.  "Metric for analyzing hit lists and pharmacophores," in Pharmacophore Perception, Development, and Use in Drug Design, G=FCner, O. F. Ed., Int. Univ. Line, 2000, La Jolla, 191-211.

Most of the above are covered in some details in "the Pharmacophore book".  Go to www.amazon.com or www.barnesandnoble.com and= search for the keyword "pharmacophore."  A detailed review= of the book (written by Lisa Balbes) can be found at ChemWeb http://www.chemweb.com/alchem/2000/books/bk_000728_osm= an.html

As far as conformational diversity, see the following three= papers and references within:

Smellie, A.; Teig, S. L.; Towbin, P. "Poling:= Promoting Conformational Coverage", J. Comp. Chem.,= 1995, 16, 171-187.

Smellie, A.; Kahn, S. D.; Teig, S.  "An Analysis of Conformational= Coverage 1. Validation and Estimation of Coverage", J. Chem. Inf.= Comput. Sci., 1995, 35, 285-294.

Smellie, A.; Kahn, S. D.; Teig, S.  "An Analysis of Conformational= Coverage 2. Applications of Conformational Models", J. Chem. Inf.= Comput. Sci., 1995, 35, 295-304.

Hope this helps a bit.  Thx...osman


At 07:06 PM 8/3/00 -0400, Joe M Leonard wrote:
Folks,

When I was at ACS SF in 1997, several of us discussed whether
there were any published methods to score pharmacophores without
having to do the search(es) and compare the results.  The lunch-
consensus was that nobody had done this, and that it was an
interesting area...  Therefore, were we wrong in 1997, or has
there been work done since then that I should be aware of?


Also, I am interested in investigating conformational diversity,
and seek similar information.  I've got some ideas, but hate to
reinvent wheels...  Are there particular papers I should run
down, or people I should talk to?

Pointers, citations, whatever appreciated!  If the responses
are good, I'll summarize...

Joe

P.S. If people want to talk about this, I'll be at EuroQSAR
(and at ACS for a short while).


-=3D This is automatically added to each message by mailing script =3D-
CHEMISTRY@ccl.net -- To Everybody    |  = CHEMISTRY-REQUEST@ccl.net -- To Admins
MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
CHEMISTRY-SEARCH@ccl.net -- archive search   = |    Gopher: gopher.ccl.net 70
Ftp: ftp.ccl.net = |  WWW: http://www.ccl.net/chemistry/  | Jan:= jkl@ccl.net





---
Osman F. G=FCner, Ph.D.
Director,  Lead Identification & Optimization
Molecular Simulations Inc.   (858) 799-5341
osman@msi.com        http://www.msi.com --=====================_438059==_.ALT--