From chemistry-request@www.ccl.net Mon Jan 25 03:37:43 1999 Received: from naomi.eerie.fr ([146.19.248.22]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA02518 Mon, 25 Jan 1999 03:37:42 -0500 (EST) Received: from syntem.eerie.fr (localhost [127.0.0.1]) by naomi.eerie.fr (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id IAA07574 for ; Mon, 25 Jan 1999 08:41:03 +0100 (MET) Sender: domi@syntem.eerie.fr Message-ID: <36AC200E.AFB24EF5@syntem.eerie.fr> Date: Mon, 25 Jan 1999 08:41:02 +0100 From: Dominique Gorse Organization: Synt:em X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: SUMMARY:Algorithms for variable orthogonalization and PLS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, A lot of thanks to those who replied to my questions about variable orthogonalization and source code about Partial Least Squares. Dr. Peter Bladon : cbas25@strath.ac.uk Paul Davis : paul@pdchem.demon.co.uk Christian Pilger : cpilger@oc30.uni-paderborn.de (Organische Chemie - Uni-GH Paderborn) Dr David B. Turner : D.Turner@sheffield.ac.uk (Dept. of Information Studies University of Sheffield) I made the summary in 3 parts : References, WWW links and where to get source code. ********************** SUMMARY ********************** References about PLS: --------------------- Paul Geladi and Bruce R. Kowalski (1986), "Partial least-squares regression: a tutorial", Analytica Chimica Acta, vol 18, pg 1-17. Paul Geladi and Bruce R. Kowalski (1986), "An example of 2-block predictive partial least-squares regression with simulated data", Analytica Chimica Acta, vol 185, p19-32. W.J. Dunn, S. Wold, U. Edlund, S. Hellberg, J. Gasteiger (1984), "Multivariate Structure-Activity Relationships Between Data from a Battery of Biological Tests and an Ensemble of Structure Descriptors: The PLS Method", Quant. Struct.-Act Relat. Vol 3 p131-137. Bush, BL and Nachbar Jr, RB J. Comput.-Aided Mol. Design,7, (1993) 587-619. EXTENDING THE TREND VECTOR - THE TREND MATRIX AND SAMPLE-BASED PARTIAL LEAST-SQUARES SHERIDAN_RP, NACHBAR_RB, BUSH_BL JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1994, 8, 3, pp.323-340. Web links _________ QSAR-Server of Alex Tropsha at the Univeristy of North Carolina, Chapel Hill/NC, USA http://mmlin1.pha.unc.edu/~jin/QSAR/ Svante Wold, the fouder of UMETRI company, has been one of the major developers of PLS through the last years. http://www.umetri.se/ Source codes ___________ Peter Bladon has a program which handles QSAR data in the form of a spreadsheet, and it caters for Principal Component Analysis. This can be done in two ways: either by a full diagonalization method (Jacobi) or by Non-Iterative-Partial-Least-Squares (NIPALS). The results of PCA can be subjected to Varimax rotation and then Orthogonalization. The package is distributed in the form of Fortran-77 source code, which could be adapted for other programs. The program itself (CHEMSPREAD) will only work on Silicon Graphics machines (because the spreadsheet facilities rely on the SGI GL library). http://interchem.chem.strath.ac.uk/inter/interprobe.html PCA and PLS (NIPALS and SIMPLS) source code (Fortran) at the Jay Ponder Lab page: http://dasher/wustl.edu SAMPLS can also be purchased from QCPE: http://www.ccl.net/ccl/qcpe/QCPE/section12.html Orthogonalisation: http://www.ccl.net/ccl/qcpe/QCPE/section01.html -- **************************************************************** Dominique Gorse Synt:em Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: dgorse@syntem.eerie.fr France Tel: +33 (0)4 66 04 86 65 Fax: +33 (0)4 66 04 86 67 **************************************************************** Discover New Drugs, Discover Synt:em http://www.syntem.com **************************************************************** From chemistry-request@www.ccl.net Mon Jan 25 05:25:49 1999 Received: from jmlopez.fam.cie.uva.es (jmlopez.fam.cie.uva.es [157.88.38.56]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA02745 Mon, 25 Jan 1999 05:25:46 -0500 (EST) Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.8.3/8.8.3) id LAA04661 for chemistry@www.ccl.net; Mon, 25 Jan 1999 11:28:14 +0100 Date: Mon, 25 Jan 1999 11:28:14 +0100 From: Andres Aguado Message-Id: <199901251028.LAA04661@jmlopez.fam.cie.uva.es> To: chemistry@www.ccl.net Subject: Na_2O Dear all, I need to know references about theoretical or experimental studies of the properties of the sodium oxide molecule (Na_2O). Could someone point me to some of those references?? Thanks a lot!! Andres Aguado. e-mail:aguado@jmlopez.fam.cie.uva.es From chemistry-request@www.ccl.net Mon Jan 25 08:37:16 1999 Received: from boris.3dp.com (boris.3dp.com [207.106.4.70]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA03702 Mon, 25 Jan 1999 08:37:15 -0500 (EST) Received: from dimitris (dimitris.3dp.com [199.33.182.106]) by boris.3dp.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id IAA73800 for ; Mon, 25 Jan 1999 08:38:21 -0500 (EST) Reply-To: From: "Dimitris K. Agrafiotis" To: Subject: need tough distance geometry problems Date: Mon, 25 Jan 1999 08:42:48 -0600 Message-ID: <000501be4870$fadcbd60$6ab621c7@dimitris.3dp.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 X-Mimeole: Produced By Microsoft MimeOLE V4.72.3110.3 Importance: Normal Dear CCL members, I am looking for the toughest structure determination problems known in the literature that involve the generation of atomic coordinates from distance constraints. That would include NMR problems, protein folding and threading, conformational searching, and things of that nature. Of particular interest are problems with missing, noisy or corrupt data, and problems that are considered intractable with current techniques. Your help would be GREATLY appreciated. Thanks, --- Dimitris K. Agrafiotis, PhD | E-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | Tel: (610) 458-6045 665 Stockton Drive, Suite 104 | Fax: (610) 458-8249 Exton, PA 19341 From chemistry-request@www.ccl.net Mon Jan 25 10:47:01 1999 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA04984 Mon, 25 Jan 1999 10:47:00 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with ESMTP id QAA03756 for ; Mon, 25 Jan 1999 16:47:51 +0100 (MET) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with SMTP id QAA29241 for ; Mon, 25 Jan 1999 16:43:56 +0100 (MET) Received: by styx.bruyeres.cea.fr (CEANET-1.1+) id AA06696; Mon, 25 Jan 1999 16:46:56 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by styx via smap id sma006657; Mon Jan 25 16:46:01 1999 Received: from ripault.cea.fr (manse.ripault.cea.fr [132.165.32.9]) by ripault.cea.fr. (8.8.7/8.7.3) with ESMTP id QAA01612 for ; Mon, 25 Jan 1999 16:45:38 +0100 Received: from manse.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.7/8.8.7) with SMTP id QAA18261 for ; Mon, 25 Jan 1999 16:47:32 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <36AC9213.60F42EC3@ripault.cea.fr> Date: Mon, 25 Jan 1999 15:47:31 +0000 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.32 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Hydrogen Bonds with DFT / GGA Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Hello everybody, I have carried out some calculations of energetic data for molecules including nitroaromatics with gradient-corrected DFT functionals, especially Becke-Perdew86. The results are satisfactory excepted for tri-amino-trinitro-benzene, the only molecule in my dataset showing intramolecular hydrogen bond. I read somewhere that DFT was not very good at describing hydrogen bonds. I wonder if anybody can provide me some details about this subject, i.e. performance of DFT with regard to hydrogen bonds. Thank you. Regards -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From chemistry-request@www.ccl.net Mon Jan 25 12:24:12 1999 Received: from postal.ucc.uno.edu (postal.ucc.uno.edu [137.30.1.80]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA06310 Mon, 25 Jan 1999 12:24:11 -0500 (EST) Received: from uno.edu (linus.chem.uno.edu [137.30.57.125]) by postal.ucc.uno.edu (PMDF V5.2-29 #33240) with ESMTP id <0F64008MZLGCG7@postal.ucc.uno.edu> for chemistry@www.ccl.net; Mon, 25 Jan 1999 11:19:24 -0600 (CST) Date: Mon, 25 Jan 1999 11:21:40 -0600 From: "F. Abu-Awwad" Subject: G94 vs G98W and checkpoint files To: chemistry@www.ccl.net Message-id: <36ACA824.BC5725B2@uno.edu> MIME-version: 1.0 X-Mailer: Mozilla 4.04 [en] (Win95; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hellow I wonder if there is any way I can reuse the checkpoint files generated from G94, UNIX base, with G98W. thank you Fakhr Abu-Awwad University of New Orleans From chemistry-request@www.ccl.net Mon Jan 25 14:57:10 1999 Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA14292 Mon, 25 Jan 1999 14:57:09 -0500 (EST) Received: from physics.ucsd.edu (physics.ucsd.edu [132.239.69.26]) by mailbox2.ucsd.edu (8.9.1a/8.9.1) with SMTP id LAA18508; Mon, 25 Jan 1999 11:57:11 -0800 (PST) Received: from localhost by physics.ucsd.edu (SMI-8.6/SMI-SVR4) id LAA11288; Mon, 25 Jan 1999 11:55:30 -0800 Date: Mon, 25 Jan 1999 11:55:30 -0800 (PST) From: Margaret Cheung X-Sender: cheung@physics To: kynn@panix.com cc: chemistry@www.ccl.net Subject: Re: CCL:[Q] Histogram method In-Reply-To: <199901232316.SAA05497@panix3.panix.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, KJ, Please check out WHAM, weighted histogram method, which extrapolated the thermodynamic properties. Please check out PNAS vol 94, pp 10161 Exploring the folding free energy surface of a three-helix bundle protein by Zhuyan Guo, Charles Brooks III, and Erik Boczko. The definition of WHAM will be sited in the reference. Regards, Margaret S. Cheung Physics/Biophysics Department 0350 University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0350 On Sat, 23 Jan 1999 kynn@panix.com wrote: > > > I've come across a few papers on computational protein models that > claim to use the so-called histogram method to estimate free energies > of folding, but I don't see how they could have done this, except for > cases much more trivial than those reported. It seems to me that to > apply the histogram method, it would be necessary to run a simulation > that sampled both the folded *and* the unfolded states reasonably well > (so that the population histograms collected had any chance of > approximating the real relative probabilities of the two macrostates). > This means running the simulation at temperatures close to the folding > transition temperature, Tf. But, except for very short chains (N < > 75) or very streamlined models (cubic lattice models), > folding/unfolding events become so rare as T approaches Tf, that it > would take weeks or even months to collect the data for each > application of this method. Is this so? > > I hope I'm wrong in this assessment, and that someone would be kind > enough to clear up my confusion. Specifically, how is it possible to > use the histogram method to estimate free energies of folding > *without* collecting many folding/unfolding events near Tf? > > Thanks in advance, > > KJ > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: kynn@panix.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From chemistry-request@www.ccl.net Mon Jan 25 15:16:06 1999 Received: from tbone.agouron.com (tbone.agouron.com [198.182.177.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA16894 Mon, 25 Jan 1999 15:16:05 -0500 (EST) Received: (from gproxy@localhost) by tbone.agouron.com (8.9.1a/8.8.7) id MAA16144 for ; Mon, 25 Jan 1999 12:16:05 -0800 (PST) Received: from taz.agouron.com(10.0.63.4) via SMTP by www.ccl.net, id smtpdAAAa003vY; Mon Jan 25 12:15:58 1999 Received: by taz.agouron.com (950413.SGI.8.6.12/951211.SGI) id MAA05615; Mon, 25 Jan 1999 12:15:57 -0800 Date: Mon, 25 Jan 1999 12:15:57 -0800 Message-Id: <199901252015.MAA05615@taz.agouron.com> From: Djamal Bouzida To: cheung@physics.ucsd.edu CC: kynn@panix.com, chemistry@www.ccl.net In-reply-to: (message from Margaret Cheung on Mon, 25 Jan 1999 11:55:30 -0800 (PST)) Subject: Re: CCL:[Q] Histogram method References: KJ, You're probably thinking single histogram method and you are right in your assessment of a single run around the transition temperature . However, one can combine histogram data from multiple simulations as long as overlap exists between the various histograms. This is called the multiple histogram method which was developed by Alan Ferrenberg and Robert Swendsen, which was extended to biological systems by Kumar et al. I'll be more than happy to dig out the various references for you. Just let me know. Happy histogramming. -- Djamal Bouzida, Ph.D. Agouron Pharmaceuticals, Inc.