From chemistry-request@server.ccl.net Mon Mar 3 04:54:24 2003 Received: from yangtze.hku.hk ([147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h239sMQ28128 for ; Mon, 3 Mar 2003 04:54:23 -0500 Received: from localhost (andy@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h239REO07924 for ; Mon, 3 Mar 2003 17:29:26 +0800 Date: Mon, 3 Mar 2003 17:27:14 +0800 (HKT) From: Ng Man Fai To: CHEMISTRY@ccl.net Subject: Zindo Boron parameter Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Does anyone know the zindo boron parameters such as resonance integral, ionization potential for s and p shells, slater condon factors? Any reference suggested. Thanks a lot. Best regards, Andy From chemistry-request@server.ccl.net Mon Mar 3 03:17:31 2003 Received: from sainfoin.saclay.cea.fr ([132.166.192.126]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h238HUQ13509 for ; Mon, 3 Mar 2003 03:17:30 -0500 Received: from araneus.saclay.cea.fr (araneus.saclay.cea.fr [132.166.192.110]) by sainfoin.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Internet.1.0) with ESMTP id h238HUYG011921 for ; Mon, 3 Mar 2003 09:17:30 +0100 (MET) Received: from nenuphar.saclay.cea.fr (unverified) by araneus.saclay.cea.fr (Content Technologies SMTPRS 4.3.6) with ESMTP id ; Mon, 3 Mar 2003 09:09:25 +0100 Received: from pandora.saclay.cea.fr (pandora.saclay.cea.fr [132.166.23.28]) by nenuphar.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Interne.1.0) with ESMTP id h238HPg4018544; Mon, 3 Mar 2003 09:17:25 +0100 (MET) Received: from pandora.saclay.cea.fr (pandora.saclay.cea.fr [132.166.23.28]) by pandora.saclay.cea.fr (8.9.3/jtpda-5.3.2) with SMTP id JAA08553 ; Mon, 3 Mar 2003 09:14:32 +0100 (MET) Message-Id: <200303030814.JAA08553@pandora.saclay.cea.fr> Date: Mon, 3 Mar 2003 09:14:32 +0100 (MET) From: Rodolphe Pollet Reply-To: Rodolphe Pollet Subject: Re: CCL:sofwares for non-linear fitting!! To: chemistry@ccl.net Cc: pradipta@cgl.ucsf.edu MIME-Version: 1.0 Content-Type: TEXT/plain; charset=ISO-8859-1 Content-MD5: DuAU/FXj5a52J474L0itdw== X-Mailer: dtmail 1.2.1 CDE Version 1.2.1 SunOS 5.6 sun4u sparc Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h238HVQ13510 >From: Pradipta Bandyopadhyay >To: chemistry@ccl.net >Subject: CCL:sofwares for non-linear fitting!! > What are the best softwares (free and for UNIX) to do non-linear >fitting for a very large amount of data? gnuplot :) *********************************************************** Rodolphe POLLET EQUIPE DE CHIMIE THEORIQUE Laboratoire Francis Perrin DSM/DRECAM/SPAM Commissariat a l´Energie Atomique 91 191 Gif-sur-Yvette CEDEX Tel : 01 69 08 37 40 Fax : 01 69 08 87 07 mailto:pollet@pandora.saclay.cea.fr http://www-drecam.cea.fr/spam/themes/chimietheo/index.html *********************************************************** From chemistry-request@server.ccl.net Mon Mar 3 05:19:13 2003 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23AJDQ28912 for ; Mon, 3 Mar 2003 05:19:13 -0500 Received: from unibas.ch ([131.152.94.93]) by igor.urz.unibas.ch (PMDF V6.1-1 #40761) with ESMTP id <0HB600O7W4O0HW@igor.urz.unibas.ch> for chemistry@ccl.net; Mon, 03 Mar 2003 11:19:13 +0100 (MET) Date: Mon, 03 Mar 2003 11:19:13 +0100 From: Michele Porro Subject: Scoring To: CCL Message-id: <9490D2FE-4D61-11D7-9D01-000393913E54@unibas.ch> MIME-version: 1.0 (Apple Message framework v551) X-Mailer: Apple Mail (2.551) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7bit X-Priority: 3 Hallo everybody, could somebody of you suggest me good review-papers on scoring and scoring functions? I would like to find out which are the most used procedures to score docking results. Thank you in advace Best regards mike *************************************** Michele Porro Institute of Molecular Pharmacy Pharmacenter University of Basel Klingelbergstrasse 50 CH-4056 Basel Tel: +41 61 267 15 63 Fax: +41 61 267 15 52 e-mail: michele.porro@unibas.ch Web : www.pharma.unibas.ch **************************************** From chemistry-request@server.ccl.net Mon Mar 3 04:20:28 2003 Received: from darius.ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h239KRQ27667 for ; Mon, 3 Mar 2003 04:20:28 -0500 Received: from echo.ribotargets.com (echo [194.129.39.91]) by darius.ribotargets.com (SGI-8.9.3/8.9.3) with ESMTP id JAA01282; Mon, 3 Mar 2003 09:20:05 GMT Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18pm38-0007JD-00; Mon, 03 Mar 2003 09:15:54 +0000 Date: Mon, 3 Mar 2003 09:15:54 +0000 (GMT) From: Szilveszter Juhos To: Pradipta Bandyopadhyay cc: chemistry@ccl.net Subject: Re: CCL:sofwares for non-linear fitting!! In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > What are the best softwares (free and for UNIX) to do non-linear > fitting for a very large amount of data? Hello, non-linear fitting is a quite huge topic from fitting simple nonlinear functions to neural-net based stuff. If you have too many points, be aware of the robustness of the procedure. In short if you have too many points at some part of the data, that will be overrepresented biasing the final parameter estimates. Softwares you can try: http://www.octave.org/ "GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab." http://plasma-gate.weizmann.ac.il/Grace/ "Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace runs on practically any version of Unix-like OS. " (it also has curve fitting capabilities) http://www.gnuplot.info/ Gnuplot itself can do some nonlinear fitting, type "help fit" in its command prompt. Hope it helps: Szilva From chemistry-request@server.ccl.net Mon Mar 3 10:14:27 2003 Received: from cytosin.uni-konstanz.de ([134.34.240.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23FERQ04861 for ; Mon, 3 Mar 2003 10:14:27 -0500 Received: from comm01.rz.uni-konstanz.de (comm01.rz.uni-konstanz.de [134.34.165.4]) by cytosin.uni-konstanz.de (Postfix) with ESMTP id D9DE6E3203 for ; Mon, 3 Mar 2003 16:12:04 +0100 (MET) Received: from webct10 (webct10.chemie.uni-konstanz.de [134.34.110.160]) by lh-iplanet.rz.uni-konstanz.de (iPlanet Messaging Server 5.1 HotFix 1.5 (built Sep 23 2002)) with ESMTP id <0HB600D3OIC3YZ@lh-iplanet.rz.uni-konstanz.de> for Chemistry@ccl.net; Mon, 03 Mar 2003 16:14:27 +0100 (MET) Date: Mon, 03 Mar 2003 16:13:54 +0100 From: pop14848 Subject: HOMO/LUMO energy gap To: Chemistry@ccl.net Reply-To: eike.huebner@uni-konstanz.de Message-id: <200303031613540010.1047C436@mailhub.uni-konstanz.de> MIME-version: 1.0 X-Mailer: Calypso Version 3.30.00.00 (1) Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT References: <200302201906520439.00BAA24F@willy.chemie.uni-konstanz.de> <200302210931090125.03D1E77D@mailhub.uni-konstanz.de> Hi, can anyone point me to a paper where the reasons for the too large energy gap between calculated (Hartree-Fock) HOMO-LUMO orbitals in comparison to the longest wavelenght absorbtion is discussed? In fact I am looking not for a lot of examples or calculations but for a more general paper (which can be cited aswell) discussing why HF calculations give much too short longest wavelength absorbtions compared to the experiment. Thanks in advance Eike Huebner From chemistry-request@server.ccl.net Mon Mar 3 11:42:10 2003 Received: from patronimo.umh.ac.be ([193.190.193.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23Gg9Q08039 for ; Mon, 3 Mar 2003 11:42:09 -0500 Received: from patronimo (patronimo [193.190.193.113]) by patronimo.umh.ac.be (8.12.6/8.12.6) with ESMTP id h23GfrVn105996; Mon, 3 Mar 2003 17:41:53 +0100 Date: Mon, 3 Mar 2003 17:41:52 +0100 (NFT) From: Victor Geskin X-X-Sender: Victor@patronimo To: pop14848 cc: Chemistry@ccl.net Subject: Re: CCL:HOMO/LUMO energy gap In-Reply-To: <200303031613540010.1047C436@mailhub.uni-konstanz.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Scanned-By: MIMEDefang 2.1 (www dot roaringpenguin dot com slash mimedefang) On Mon, 3 Mar 2003, pop14848 wrote: > Hi, > > can anyone point me to a paper where the reasons for the too large > energy gap between calculated (Hartree-Fock) HOMO-LUMO orbitals in > comparison to the longest wavelenght absorbtion is discussed? In fact I > am looking not for a lot of examples or calculations but for a more > general paper (which can be cited aswell) discussing why HF calculations > give much too short longest wavelength absorbtions compared to the > experiment. > > Thanks in advance > > Eike Huebner > Hello, I am not aware of an exact reference, rather you might want to look in textbooks. As far as I understand, the reason is double. First, if we write down the HF excitation energy from orbial "i" to a virtual orbital "a", supposing them frozen, with orbial energies e(i) and e(a), we obtain: delta E(i->a)=e(a)-e(i)-, which is not simply orbital energy difference. Second, HF virtual orbital energies are unphysical themselves: one can show that e(a) includes the Coulomb repulsion with all n electrons, and not only the remaining (n-1); that is self-interaction is not excluded. This pushes virtual orbitals up in the energy scale. Sincerely, Victor. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > ___________________________________________________________________ Dr Victor GESKIN e-mail: Victor@averell.umh.ac.be Service de Chimie http://morris.umh.ac.be des Materiaux Nouveaux Universite de Mons-Hainaut phone: +32-(0)65.37.38.67 Place du Parc, 20 fax: +32-(0)65.37.38.61 B-7000 MONS, BELGIQUE GSM: +32-(0)486.779.799 ___________________________________________________________________ From jkl@ccl.net Mon Mar 3 13:46:30 2003 -0500 Reply-To: From: "Mark Thompson" To: "Michele Porro" , "CCL" Subject: RE: Scoring Date: Mon, 3 Mar 2003 09:31:20 -0800 Message-ID: <002b01c2e1aa$b48462a0$0300a8c0@attbi.com> Dear Mike, A very good recent review is: "The Use of Scoring Functions in Drug Discovery Applications" Hans-Joachim Bohm and Martin Stahl Reviews in Computational Chemistry Vol 18, pp 41-87 Eds. Kenny B. Lipkowitz and Donald B. Boyd Wiley-VCH, 2002 Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Michele Porro > Sent: Monday, March 03, 2003 2:19 AM > To: CCL > Subject: CCL:Scoring > > > Hallo everybody, > could somebody of you suggest me good > review-papers on scoring and > scoring functions? I would like to find out which are the most used > procedures to score docking results. > Thank you in advace > Best regards > mike > > *************************************** > Michele Porro > Institute of Molecular Pharmacy > Pharmacenter > University of Basel > Klingelbergstrasse 50 > CH-4056 Basel > Tel: +41 61 267 15 63 > Fax: +41 61 267 15 52 > e-mail: michele.porro@unibas.ch > Web : www.pharma.unibas.ch > **************************************** > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- > To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon Mar 3 09:42:30 2003 Received: from kelly.bath.ac.uk ([138.38.32.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23EgTQ03893 for ; Mon, 3 Mar 2003 09:42:29 -0500 Received: from mmdf by kelly.bath.ac.uk with pleasure id 18pr9A-00086W-01 for chemistry@ccl.net; Mon, 03 Mar 2003 14:42:28 +0000 Received: from midge.bath.ac.uk ([138.38.32.34] ident=mmdf) by kelly.bath.ac.uk with smtp id 18pr97-0002lZ-01; Mon, 03 Mar 2003 14:42:25 +0000 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by bath.ac.uk id aa15632 ; 3 Mar 2003 14:42 +0000 From: James Robinson To: Michele Porro , CCL Subject: RE: Scoring Date: Mon, 3 Mar 2003 14:45:24 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: <9490D2FE-4D61-11D7-9D01-000393913E54@unibas.ch> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h23EgUQ03894 Some general papers I would suggest... 1. Current Opinion in Structural Biology, Volume 11, Issue2, 1 April 2001, pp. 231- 235. G. ... "Statistical potenetials and scoring functions applied to protein-ligand binding." H Gohlke, G Klebe. 2. Current Opinion in Chemical Biology, Volume5, issue4,1 august 2001, p. 375 - 382. " High-throughput docking for lead generation" R Abagyan, M Totrov. 3. Il Farmaco, vol 57, issue3, March 2002, p. 243 - 251. "Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design" C Sotriffer and G Klebe. James Robinson Bath University -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Michele Porro Sent: 03 March 2003 10:19 To: CCL Subject: CCL:Scoring Hallo everybody, could somebody of you suggest me good review-papers on scoring and scoring functions? I would like to find out which are the most used procedures to score docking results. Thank you in advace Best regards mike *************************************** Michele Porro Institute of Molecular Pharmacy Pharmacenter University of Basel Klingelbergstrasse 50 CH-4056 Basel Tel: +41 61 267 15 63 Fax: +41 61 267 15 52 e-mail: michele.porro@unibas.ch Web : www.pharma.unibas.ch **************************************** -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Mar 3 11:23:10 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23GNAQ07569 for ; Mon, 3 Mar 2003 11:23:10 -0500 Reply-To: "Elizabeth Crookenden" To: CHEMISTRY@ccl.net Cc: Elizabethc@accelrys.com Subject: Accelrys Customer Training for May MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: "Jeff Nauss" Date: Mon, 3 Mar 2003 08:23:09 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 03/03/2003 08:23:11 AM, Serialize complete at 03/03/2003 08:23:11 AM Content-Type: text/plain; charset="us-ascii" Accelrys Inc. are holding the following training workshops at locations in the US and Europe during May 2003. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $450 per day for government and $330 per day for academic. Macromolecular Modeling: Introduction to Life Science Modeling with InsightII 6th-7th May Cambridge, UK Homology Base Protein Design 8th-9th May Cambridge UK CHARMm 12th-13th May Cambridge UK Structure Based Drug Design with InsightII 14th-15th May Cambridge, UK For course details and registration see: http://www.accelrys.com/training/macro/schedule.html Cheminformatics: DS Accord Enterprise OMNIS Client 6th May San Diego, CA RS3 for Excel 7th May San Diego, CA RS3 Inventory 8th May, San Diego, CA OMMM 9th May San Diego, CA DIVA 12th May San Diego, CA DS Accord Biostore Database Administration 13th-14th May San Diego,CA Accord for Excel 28th May San Diego, CA Accord for Access 29th May San Diego, CA Accord Database Explorer 30th May San Diego, CA For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html Rational Drug Design: Introduction to Cerius2 for Life Sciences 20th-21st May Cambridge, UK Library Design and Analysis 22nd-23rd May Cambridge, UK For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html Elizabeth Crookenden Training Co-ordinator Accelrys Ltd 334 Cambridge Science Park Cambridge CB4 0WN UK Telephone number: +44 (0) 1223 228691 Fax number: +44 (0) 1223 228501 Web: http://www.accelrys.com -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Mon Mar 3 13:39:17 2003 Received: from artemis.rus.uni-stuttgart.de ([129.69.1.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23IdGQ10764 for ; Mon, 3 Mar 2003 13:39:16 -0500 Received: from po.uni-stuttgart.de (samurei.biologie.uni-stuttgart.de [129.69.145.3]) by artemis.rus.uni-stuttgart.de with ESMTP id TAA07568 for ; Mon, 3 Mar 2003 19:39:11 +0100 (MET) env-from (itbsta@po.uni-stuttgart.de) Message-ID: <3E63A152.2050406@po.uni-stuttgart.de> Date: Mon, 03 Mar 2003 19:39:14 +0100 From: "Stephan.Tatzel" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; de-DE; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: de-de, de MIME-Version: 1.0 To: CCL-List Subject: Trajectory Output with AutoDock 3. Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Hi all, did anyone tried to generate trajectories during a simulated annealing run with AutoDock? I have problems to generate trajectory coordinates for every cycle of a run. For an example I set the following parameters in the docking parameter file: runs 3 # number of runs cycles 50 # cycles accs 300 # steps accepted rejs 300 # steps rejected select m # minimum or last outlev 1 # diagnostic output level trjfrq 1 # trajectory frequency trjout test.trj # trajectory file trjsel E # A=acc only;E=either acc or r I also tried several values for trjbeg and trjend , but in every case I got an output with only the values for the first cycle of every run like this: ntorsions 0 run 1 cycle 1 temp 1000.000000 state 1 R 131808.296875 0.000000 45.497338 64.274652 30.326107 -0.668758 -0.623915 -0.404342 86.532517 state 2 e 1000.000000 1000.000000 47.229206 62.321471 32.220805 -0.668758 -0.623915 -0.404342 86.532517 &&& state 304 R 186972.781250 0.000000 47.336364 65.528870 34.041372 -0.668758 -0.623915 -0.404342 86.532517 ntorsions 0 run 2 cycle 1 temp 1000.000000 state 1 e 1000.000000 1000.000000 59.229028 58.824385 45.100996 -0.248347 0.186834 0.950482 240.451190 &&&.. .............. Why isnt it possible to get the coordinates for the states of the other 49 cycles of every run? Thanks in advance for your help. Stephan -- _________________________________________________ Stephan Tatzel Institute of Technical Biochemistry University of Stuttgart Allmandring 31 D-70569 Stuttgart, Germany Email: Stephan.Tatzel@po.uni-stuttgart.de From chemistry-request@server.ccl.net Mon Mar 3 17:59:29 2003 Received: from fulcrum.physbio.mssm.edu ([146.203.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23MxTQ16193 for ; Mon, 3 Mar 2003 17:59:29 -0500 Received: from mezei (helo=localhost) by fulcrum.physbio.mssm.edu with local-esmtp (Exim 3.11 #1) id 18pyu9-00dYYo-00 for CHEMISTRY@ccl.net; Mon, 03 Mar 2003 17:59:29 -0500 Date: Mon, 3 Mar 2003 17:59:29 -0500 From: Mihaly Mezei X-X-Sender: mezei@fulcrum.physbio.mssm.edu To: Computationl Chemistry List Subject: Charmm29/f90/SGI Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Mihaly Mezei Greetings! we are getting a bus error when trying to compile Charmm 29 on an SGI. If you suceeded in such a compilation, could you tell us the trick? Thanks, regads: Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of Medicine Voice: (212) 241-2186 Fax: (212) 860-3369| WWW (MSSM home): http:// adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei From chemistry-request@server.ccl.net Mon Mar 3 15:47:28 2003 Received: from master.iums.ac.ir ([194.225.184.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23KlPQ13322 for ; Mon, 3 Mar 2003 15:47:27 -0500 Received: from amshome.iums.ac.ir ([194.225.184.156]) by master.iums.ac.ir with Microsoft SMTPSVC(5.0.2195.5329); Tue, 4 Mar 2003 01:20:13 +0430 Message-Id: <5.0.2.1.2.20030304011028.03878070@pop3.iums.ac.ir> X-Sender: armin@pop3.iums.ac.ir X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Tue, 04 Mar 2003 01:17:07 +0430 To: CHEMISTRY@ccl.net From: "Armin M. Sobhani" Subject: Re: CCL:Scoring Cc: Michele Porro In-Reply-To: <9490D2FE-4D61-11D7-9D01-000393913E54@unibas.ch> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-OriginalArrivalTime: 03 Mar 2003 20:50:14.0515 (UTC) FILETIME=[7D809C30:01C2E1C6] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h23KlSQ13329 Dear Mike, For another good recent review try this: Halperin I, Ma B, Wolfson H and Nussinov R. "Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions", PROTEINS: Structure, Function, and Genetics, 2002; 47:409-443 Armin At 11:19 Þ.Ù 2003/03/03 +0100, you wrote: >Hallo everybody, > could somebody of you suggest me good > review-papers on scoring and scoring functions? I would like to find out > which are the most used procedures to score docking results. >Thank you in advace >Best regards >mike p-----__---_________----____----------------------------------------q | / \ / _ _ \ / ____\ Armin M. Sobhani, PharmD, PhD | | / \\ \\ \\ \/\ \___/_ Assitant Prof., Pharmacology Dept. | | / /\ \\ \\ \\ \ \_____ \ Iran University of Medical Sciences| | ( ___ \\ \\ \\ \/____/\ \ mailto:armin@iums.ac.ir | |( \__\_/\__\\__\\__\\__\/\_____/ Tel: +98 (21) 805 2265, Fax: ~64 | | \/__/ \/__//__//__//__/\/____/ P.O.Box: 14155-6183, Tehran, IRAN | |~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| | Once you understand the universe at the atomic level everything | | else is easy. -Richard P. Feynman | b-------------------------------------------------------------------d From chemistry-request@server.ccl.net Mon Mar 3 15:12:23 2003 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23KCNQ12787 for ; Mon, 3 Mar 2003 15:12:23 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout4.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.12) with ESMTP id h23KCFHV023445 for ; Mon, 3 Mar 2003 12:12:15 -0800 Received: from DGVR6B21 ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with SMTP id h23KCFwZ015788 for ; Mon, 3 Mar 2003 12:12:15 -0800 Message-ID: <00bb01c2e1c1$317fc4f0$74805f80@DGVR6B21> From: "Carsten Detering" To: Subject: CCL:Scoring Date: Mon, 3 Mar 2003 21:12:19 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00B8_01C2E1C9.9331B660" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_00B8_01C2E1C9.9331B660 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Michele, try these: B=F6hm, H.-J. (1994). "The development of a simple empirical scoring = function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure." J. Comp. Aid. Mol. Des. 8: 243-256. B=F6hm, H.-J. and M. Stahl (1999). "Rapid Empirical Scoring Functions in Virtual Screening Applications." Med. Chem. Res. 9(7/8): 445-462. Charifson, P. S., J. J. Corkery, et al. (1999). "Consensus Scoring: A = Method for Obtaining Improved Hit Rates from Docking Databases of = Three-Dimensional Structures into Proteins." J. Med. Chem. 42: 5100-5109. Eldridge, M. D., C. W. Murray, et al. (1997). "Empirical scoring = functions: I. The development of a fast empirical scoring funciton to estimate the binding affinity of ligands in receptor complexes." J. Comp. Aid. Mol. = Des. 11: 425-445. Gohlke, H., M. Hendlich, et al. (2000). "Knowledge-based Scoring = Function to Predict Protein-Ligand Interactions." J. Mol. Biol. 295: 337-356. Gohlke, H. and G. Klebe (2001). "Statistical potentials and scoring functions applied to protein-ligand binding." Curr. Opin. Struct. Biol. = 11: 231-235. Grzybowski, B. A., A. V. Ishchenko, et al. (2002). "From knowledge-based potentials to combinatorial lead design in silico." Acc Chem Res 35(5): 261-9. Muegge, I. and Y. C. Martin (1999). "A General and Fast Scoring Funciton = for Protein-Lignad Interactions: A Simplified Potential Approach." J. Med. = Chem. 42: 791-804. Muegge, I., Y. C. Martin, et al. (1999). "Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein." J Med Chem 42(14): 2498-503. Muegge, I. and M. Rarey (2001). Small Molecule Docking and Scoring. = Reviews in Computational Chemistry. K. B. Lipkowitz and D. B. Boyd. New York, Wiley-VCH. 17: 1-60. Tame, J. R. H. (1999). "Scoring functions: A view from the bench." J. = Com. Aid. Mol. Des. 13: 99-108. Oprea, T. I. and G. R. Marshall (1998). "Receptor-based Prediciton of = Binding Affinities." Persp. Drug Disc. Des. 9/10/11: 35-61. Hope this helps. Carsten ----- Original Message ----- From: "Michele Porro" To: "CCL" Sent: Monday, March 03, 2003 11:19 AM Subject: CCL:Scoring > Hallo everybody, > could somebody of you suggest me good review-papers on scoring and > scoring functions? I would like to find out which are the most used > procedures to score docking results. > Thank you in advace > Best regards > mike > > *************************************** > Michele Porro > Institute of Molecular Pharmacy > Pharmacenter > University of Basel > Klingelbergstrasse 50 > CH-4056 Basel > Tel: +41 61 267 15 63 > Fax: +41 61 267 15 52 > e-mail: michele.porro@unibas.ch > Web : www.pharma.unibas.ch > **************************************** > > > > -=3D This is automatically added to each message by mailing script = =3D- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ------=_NextPart_000_00B8_01C2E1C9.9331B660 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi=20 Michele,



try these:

B=F6hm, H.-J. (1994). "The = development=20 of a simple empirical scoring function
to estimate the binding = constant for a=20 protein-ligand complex of known
three-dimensional structure." J. = Comp. Aid.=20 Mol. Des. 8: 243-256.

B=F6hm, H.-J. and M. Stahl (1999). "Rapid = Empirical=20 Scoring Functions in
Virtual Screening Applications." Med. Chem. Res. = 9(7/8):=20 445-462.

Charifson, P. S., J. J. Corkery, et al. (1999). = "Consensus=20 Scoring: A Method
for Obtaining Improved Hit Rates from Docking = Databases of=20 Three-Dimensional
Structures into Proteins." J. Med. Chem. 42:=20 5100-5109.

Eldridge, M. D., C. W. Murray, et al. (1997). = "Empirical=20 scoring functions:
I. The development of a fast empirical scoring = funciton to=20 estimate the
binding affinity of ligands in receptor complexes." J. = Comp.=20 Aid. Mol. Des.
11: 425-445.

Gohlke, H., M. Hendlich, et al. = (2000).=20 "Knowledge-based Scoring Function to
Predict Protein-Ligand = Interactions." J.=20 Mol. Biol. 295: 337-356.

Gohlke, H. and G. Klebe (2001). = "Statistical=20 potentials and scoring
functions applied to protein-ligand binding." = Curr.=20 Opin. Struct. Biol. 11:
231-235.

Grzybowski, B. A., A. V. = Ishchenko,=20 et al. (2002). "From knowledge-based
potentials to combinatorial lead = design=20 in silico." Acc Chem Res 35(5):
261-9.

Muegge, I. and Y. C. = Martin=20 (1999). "A General and Fast Scoring Funciton for
Protein-Lignad = Interactions:=20 A Simplified Potential Approach." J. Med. Chem.
42: = 791-804.

Muegge,=20 I., Y. C. Martin, et al. (1999). "Evaluation of PMF scoring = in
docking weak=20 ligands to the FK506 binding protein." J Med Chem=20 42(14):
2498-503.

Muegge, I. and M. Rarey (2001). Small = Molecule=20 Docking and Scoring. Reviews
in Computational Chemistry. K. B. = Lipkowitz and=20 D. B. Boyd. New York,
Wiley-VCH. 17: 1-60.

Tame, J. R. H. = (1999).=20 "Scoring functions: A view from the bench." J. Com.
Aid. Mol. Des. = 13:=20 99-108.

Oprea, T. I. and G. R. Marshall (1998). "Receptor-based Prediciton of = Binding=20 Affinities." Persp. Drug Disc. Des. 9/10/11: 35-61.



Hope this helps.
Carsten


----- = Original=20 Message -----
From: "Michele Porro" <michele.porro@unibas.ch>
To: "CCL" <chemistry@ccl.net>
Sent: Monday, March 03, 2003 = 11:19=20 AM
Subject: CCL:Scoring


> Hallo = everybody,
>  =20 could somebody of you suggest me good review-papers on scoring = and
>=20 scoring functions? I would like to find out which are the most = used
>=20 procedures to score docking results.
> Thank you in advace
> = Best=20 regards
> mike
>
>=20 ***************************************
> Michele Porro
> = Institute=20 of Molecular Pharmacy
> Pharmacenter
> University of = Basel
>=20 Klingelbergstrasse 50
> CH-4056 Basel
> Tel:  +41 61 = 267 15=20 63
> Fax: +41 61 267 15 52
> e-mail: michele.porro@unibas.ch
> Web : www.pharma.unibas.ch
>=20 ****************************************
>
>
>
> = -=3D This=20 is automatically added to each message by mailing script =3D-
> = CHEMISTRY@ccl.net -- To=20 Everybody  | CHEMISTRY-REQUEST@ccl.net -- To
Admins
> Ftp: = ftp.ccl.net  | =20 WWW: http://www.ccl.net/chemistry/   | Jan:
jkl@ccl.net
>
>
>
>
>
------=_NextPart_000_00B8_01C2E1C9.9331B660--