From wdi@TORVS.CCC.Uni-Erlangen.DE Fri Sep 12 06:23:43 1997 Received: from enar.organik.uni-erlangen.de for wdi@TORVS.CCC.Uni-Erlangen.DE by www.ccl.net (8.8.3/950822.1) id FAA22739; Fri, 12 Sep 1997 05:35:03 -0400 (EDT) Received: from schiele (schiele.organik.uni-erlangen.de) by enar.organik.uni-erlangen.de with SMTP id AA15891 for CHEMISTRY@www.ccl.net (5.65c/IDA-1.4.4/bs-02); Fri, 12 Sep 1997 11:34:43 +0200 Received: by schiele (951211.SGI.8.6.12.PATCH1502/951211.SGI) id LAA05836; Fri, 12 Sep 1997 11:34:41 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9709121134.ZM5834@eros.ccc.uni-erlangen.de> Date: Fri, 12 Sep 1997 11:34:40 -0600 In-Reply-To: Ray Crawford "CCL:Re: CCL:NCI SMILES Database" (Sep 9, 22:14) References: Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Ray Crawford Subject: Re: CCL:Re: CCL:NCI SMILES Database Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Sep 9, 22:14, Ray Crawford wrote: > Subject: CCL:Re: CCL:NCI SMILES Database > > All, > > Marc C. Nicklaus & Bruno Bienfait raised an interesting point... It is > difficult to do string comparisons with SMILES... Does anyone know of any > utilities available that can do this quickly and painlessly? > > Thanks, > Ray Crawford > The P&G Co. > Sure. The CACTVS toolkit programs (which was used to create one of the datasets) can read and compare SMILES-encoded structures. Note however that this is not a string-level comparison but operates on the decoded structures. Therefore, it is several magnitudes slower than simple string matching (but probably still fast enough for most applications). The alternative is USMILES (Unique SMILES), a procedure to generate a unique SMILES string, regardless of the order of atoms in the structure etc. Unfortunately, as far as I know, the precise mechanism to generate this string is unpublished and proprietory to Daylight. If I am wrong with this, I'd be interested in a reference. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From mebel@linsgi.iams.sinica.edu.tw Fri Sep 12 07:23:43 1997 Received: from linsgi.iams.sinica.edu.tw for mebel@linsgi.iams.sinica.edu.tw by www.ccl.net (8.8.3/950822.1) id HAA22949; Fri, 12 Sep 1997 07:08:27 -0400 (EDT) Received: by linsgi.iams.sinica.edu.tw (940816.SGI.8.6.9/930416.SGI.AUTO) id TAA06982; Fri, 12 Sep 1997 19:05:44 -0700 Date: Fri, 12 Sep 1997 19:05:41 -0700 (PDT) From: "A. Mebel" To: hxt10@po.CWRU.Edu cc: Computational Chemistry List Subject: Re: CCL:vibronic coupling matrix elements Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr./Mr./Ms. Tsai: You can find the answer on your question in our recent paper: Chemical Physics Letters 274, 281 (1997). Sincerely, Dr. Alexander M. Mebel. Gavin Tsai wrote: Hi, CCLers: Is there any program which can calculate vibronic coupling matrix elements? Any reference or suggestion is also welcomed. Gavin Tsai From JANET.CICARIELLO-COOK@roche.com Fri Sep 12 10:23:45 1997 Received: from gatekeeper.roche.com for JANET.CICARIELLO-COOK@roche.com by www.ccl.net (8.8.3/950822.1) id JAA23461; Fri, 12 Sep 1997 09:31:50 -0400 (EDT) Received: by gatekeeper.roche.com (5.65v3.2/fma-120691); id AA27810; Fri, 12 Sep 1997 09:29:56 -0400 Received: from rnuc01.nut.roche.com by mailgate.roche.com; (5.65v3.2/1.1.8.2/20Mar96-0227PM) id AA15852; Fri, 12 Sep 1997 09:31:52 -0400 Received: from mr.nut.roche.com by Roche.COM (PMDF V5.1-8 #22401) id <01INJTQ4P68WQO6FU6@Roche.COM> for chemistry@www.ccl.net; Fri, 12 Sep 1997 09:30:40 EDT Received: with PMDF-MR; Fri, 12 Sep 1997 09:25:27 -0400 (EDT) Mr-Received: by mta RNIS08; Relayed; Fri, 12 Sep 1997 09:25:27 -0400 Mr-Received: by mta RNUC01; Relayed; Fri, 12 Sep 1997 09:30:20 -0400 Alternate-Recipient: prohibited Date: Fri, 12 Sep 1997 09:25:27 -0400 (EDT) From: JANET CICARIELLO-COOK 57165 Subject: Re: CCL: NCI SMILES Database To: Comp Chem List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Posting-Date: Fri, 12 Sep 1997 09:25:30 -0400 (EDT) Importance: normal Priority: normal Ua-Content-Id: E1808IAD20VL5 X400-Mts-Identifier: [;72529021907991/816607@RNISD0] A1-Type: MAIL Hop-Count: 2 Hi All, Ray Crawford wrote: >>Marc C. Nicklaus & Bruno Bienfait raised an interesting point... It is >>difficult to do string comparisons with SMILES... Does anyone know of any >>utilities available that can do this quickly and painlessly? Since SMILES strings are *not* unique, this can be a problem (several possible strings for any given structure). I would suggest using SLN strings instead. I know the ones in SYBYL are unique, I think others may be too (ChemDraw? for example). Janet ********************************************* * Janet Cicariello-Cook, Ph.D. * * Hoffmann-LaRoche, Inc. * * 340 Kingsland St. * * Nutley, NJ 07110 * * ph: (201) 235-7165 * * fax: (201) 235-7292 * * e-mail: janet.cicariello-cook@roche.com * ********************************************* From intsim.com!haun@news.cts.com Fri Sep 12 13:23:45 1997 Received: from mailhub.cts.com for intsim.com!haun@news.cts.com by www.ccl.net (8.8.3/950822.1) id NAA24405; Fri, 12 Sep 1997 13:13:45 -0400 (EDT) Received: from donews.cts.com(really [192.188.72.21]) by mailhub.cts.com via smail with smtp id for ; Fri, 12 Sep 97 10:13:39 -0700 (PDT) (Smail-3.1.92 1996-Mar-19 #3 built 1996-Apr-21) Received: from intsim.com by donews.cts.com with uucp (Smail3.1.29.1 #5) id m0x9ZHm-00006dC; Fri, 12 Sep 97 10:13 PDT Received: from topi.intsim.com by zebra.intsim.com via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA04091; Fri, 12 Sep 97 10:07:32 -0700 Message-Id: <2.2.32.19970912171444.0069d858@zebra.intsim.com> X-Sender: haun@zebra.intsim.com X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 12 Sep 1997 10:14:44 -0700 To: chemistry@www.ccl.net. From: Dan Haun Subject: SCULPT revision 2.1 for the SGI Dear Netters, Interactive Simulations is pleased to announce the long awaited release of revision 2.1 for the SGI. The new features for the SGI revision include: - New simplified user interface. Easier to use, improved look, icon driven, deals with aspect ratio in the graphics. -The ability to load multiple data-sets into a Sculpt session by merging files together. -Tethers (double ended springs). - Support for super-imposing multiple small molecules. - Improved force field model for small molecules. - Side by side stereo (in addition to CrystalEyes stereo). - High quality rendering (user selectable). - Improved PDB reading. - Improved documentation (full manual on-line). - Improved performance. - Compatiblity with Mac and Windows Sculpt v2.1. SCULPT will still give you the capabilities of overlaying, twisting and turning molecular structures, docking of ligands, minimizing in real time visualizing Van der Waals forces and Hydrogen Bond Electrostatics For a free trial, please visit our web site at www.intsim.com or conctact us directly at 1-888-2-SCULPT. Sincerely yours, Daniel P. Haun Tel: (619) 658-9462 Interactive Simulations Inc. Toll Free: (888) 272-8578 5330 Carroll Canyon Rd. Email: haun@intsim.com San Diego, CA 92121 Fax: (619) 658-9463 Web site http://www.intsim.com From joerg@still3.chem.columbia.edu Fri Sep 12 14:23:44 1997 Received: from mailrelay1.cc.columbia.edu for joerg@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id NAA24522; Fri, 12 Sep 1997 13:49:30 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id NAA04383 for <@smtp.columbia.edu:CHEMISTRY@www.ccl.net>; Fri, 12 Sep 1997 13:49:31 -0400 (EDT) Received: from still3 by still3.chem.columbia.edu via SMTP (950413.SGI.8.6.12/930416.SGI.AUTO) for id NAA17349; Fri, 12 Sep 1997 13:49:30 -0400 Sender: joerg@still3.chem.columbia.edu Message-ID: <341980AA.15FB@still3.chem.columbia.edu> Date: Fri, 12 Sep 1997 13:49:30 -0400 From: Joerg Weiser Organization: Columbia University X-Mailer: Mozilla 3.01Gold (X11; I; IRIX64 6.2 IP25) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Recognition of compounds from a connection table References: <199707152152.AA20799@interlock.amoco.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Member: Do you know of any references that deal with the recognition of compounds (e.g stored in a compound library) from their connection tables? Any leads would be gratefully appreciated! Thanks. I will summarize. -- ================================================================ Joerg Weiser phone: +1 212 8545143 Department of Chemistry +1 212 8548402 Columbia University 3000 Broadway MC 3140 fax: +1 212 6789039 New York, NY 10027 email: joerg@still3.chem.columbia.edu ================================================================ From PEARLMAN@VAX.PHR.UTEXAS.EDU Fri Sep 12 16:23:50 1997 Received: from VAX.PHR.UTEXAS.EDU for PEARLMAN@VAX.PHR.UTEXAS.EDU by www.ccl.net (8.8.3/950822.1) id PAA24834; Fri, 12 Sep 1997 15:26:16 -0400 (EDT) From: Date: Fri, 12 Sep 1997 14:26:10 -0500 (CDT) To: CHEMISTRY@www.ccl.net Message-Id: <970912142610.1ca5e@VAX.PHR.UTEXAS.EDU> Subject: Comparing SMILES strings Hello -- Ray Crawford recently asked how to ascertain whether two SMILES strings represent the same structure. Wolf-D. Ihlenfeldt noted that the CACTVS toolkit could perform this task but at a rate "several orders of magnitude slower" than the obvious alternative of comparing the "unique SMILES" equivalents of the two original SMILES strings. However, he suspected that the "uniqetization" (Daylight's term) algorithm was proprietary and unpublished. Although Daylight and Daylight personnel are very generous in sharing their technology, papers on the SMILES notation itself and a method for generating canonically unique SMILES strings are amongst the very few examples of their formal publications. The paper describing the generation of unique SMILES is: D. Weininger, A. Weininger, and J. L. Weininger(*), SMILES. 2. Algorithm for Generation of Unique SMILES Notation, JCICS, 29, 97-101, 1989. The corresponding author, Joe Weininger, was the father of Dave and Art who developed the algorithm and wrote the corresponding code. Unfortunately, the paper was written before SMILES notation supported stereochemical qualifiers. It is not difficult to extend the published algorithm to include stereochemistry but, as far as I know, that extension has not been published. Since, I believe, the NCI database does not include stereochemical indicators, this would not be a problem for the original questioner (who asked about comparing alternative SMILES for structures in the NCI database). However, for general applications, alternative ways of indicating the same stereochemistry must be addressed in order to assure complete and accurate comparisons. Obviously, the Daylight Toolkit (distributed by Daylight) includes code to facilitate the comparison of stereochemically-qualified SMILES strings. Those interested in developing their own code should first contact Daylight to see if they can provide advice. Failing that, interested parties can contact me directly (*not* via the CCL). -- Bob Pearlman Robert S. Pearlman, Ph.D Coulter R. Sublett Regents Chair in Pharmacy and Director, Laboratory for Molecular Graphics and Theoretical Modeling College of Pharmacy University of Texas Austin, Texas 78712 512-471-3383 (voice) 512-471-7474 (FAX) pearlman@vax.phr.utexas.edu From brian@bert.chem.wsu.edu Fri Sep 12 18:23:49 1997 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.8.3/950822.1) id RAA25389; Fri, 12 Sep 1997 17:44:45 -0400 (EDT) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.8.5/8.8.5) with SMTP id OAA11697 for ; Fri, 12 Sep 1997 14:44:08 -0700 (PDT) Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA17963; Fri, 12 Sep 1997 14:44:15 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9709122144.AA17963@bert.chem.wsu.edu> Subject: Summary:Metalloproteins To: CHEMISTRY@www.ccl.net (Computational Chemistry List) Date: Fri, 12 Sep 1997 14:44:14 -0700 (PDT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Last week some time, I asked about the fraction of PDB proteins that are metal binding. Jian Li of Scripps told me about the following issue of Chem. Reviews and in particular the introductory article by Holm et al. AUTHOR Holm, Richard H.; Kennepohl, Pierre; Solomon, Edward I. TITLE Structural and functional aspects of metal sites in biology. APPEARS IN Chemical Reviews 1996, v96n7, Nov p. 2239-2314 (75 pages) ABSTRACT A classification and structure/function analysis of native metal sites based on the functions of the five basic types of a protein-bound metal site is presented. These considerations are largely confined to the sites themselves. In this artcile the authors state that 1/3 of all proteins and enzyme require metal cofactors for biological function and that as of Dec 1995, 52% of the PDB structures contain metals (excluding weakly bound metals such as sodium). -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | || Biochem/Biophysics | brian@bert.chem.wsu.edu | || \\ WSU || Washington St. Univ| brian_beck@wsu.edu | |\ - *|| 639 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA, USA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From jsb2@camsoft.com Fri Sep 12 18:39:45 1997 Received: from camsoft.com for jsb2@camsoft.com by www.ccl.net (8.8.3/950822.1) id RAA25336; Fri, 12 Sep 1997 17:33:57 -0400 (EDT) From: Date: Fri, 12 Sep 97 17:33:57 EDT Received: by camsoft.com (4.1/3.1.090690-CambridgeSoft Corp.) id AA05152; Fri, 12 Sep 97 17:33:57 EDT Message-Id: <9709122133.AA05152@camsoft.com> To: iguana@one.net, wdi@eros.ccc.uni-erlangen.de Subject: Re: CCL:NCI SMILES Database Cc: CHEMISTRY@www.ccl.net, JANET.CICARIELLO-COOK@roche.com >>Marc C. Nicklaus & Bruno Bienfait raised an interesting point... It >>is difficult to do string comparisons with SMILES... Does anyone know >>of any utilities available that can do this quickly and painlessly? > >Sure. The CACTVS toolkit programs (which was used to create one of >the datasets) can read and compare SMILES-encoded structures. > >Note however that this is not a string-level comparison but >operates on the decoded structures. Therefore, it is several >magnitudes slower than simple string matching (but probably >still fast enough for most applications). ChemOffice can do this as well, so I did (and yes, it is *much* slower than text matching -- a little over 100 SMILES pairs per minute). For the first 1000 entries, 26 were structurally different between the SMILES strings generated by CACTVS and those generated by Babel. In each case, those generated by CACTVS were superior (which would have been my guess before starting, anyway). Of the differences, 23 involved charged structures, which Babel neutral-ized. Additionally, Babel seems not to be real fond of mercury atoms. Other differences include different aromaticity-perception algorithms. The algorithm used by CACTVS is closer to the one used by Daylight. However, since the SMILES spec defines the delocalized (c1ccccc1) as absolutely equivalent to the Kekule version (C1=CC=CC=C1), this is not a big deal. For that matter, it's not really clear why either program bothers to attempt aromaticity perception if they're not doing Unique SMILES. I guess it looks nice, but as far as the SMILES definition goes, it's not relevent. >Since SMILES strings are *not* unique, this can be a problem (several >possible strings for any given structure). I would suggest using SLN >strings instead. I know the ones in SYBYL are unique, I think others >may be too (ChemDraw? for example). SLN strings come in unique and non-unique versions, just as do SMILES strings. ChemDraw generates non-unique versions for both. Ideally, NCI will provide the raw connection tables for this new data set, as they did several years ago for their 127,000-compound collection. Each format conversion has potential for introducing problems, so the fewer, the better. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com