From chemistry-request@server.ccl.net Wed Jun 12 00:04:49 2002 Received: from alchemy.chem.utoronto.ca (IDENT:root@[142.150.224.224]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C44nj09279 for ; Wed, 12 Jun 2002 00:04:49 -0400 Received: from localhost (cmatta@localhost) by alchemy.chem.utoronto.ca (8.11.6/8.11.6) with ESMTP id g5C44md17059 for ; Wed, 12 Jun 2002 00:04:48 -0400 Date: Wed, 12 Jun 2002 00:04:48 -0400 (EDT) From: "Cherif F. Matta" X-X-Sender: cmatta@alchemy To: CHEMISTRY@ccl.net Subject: Si(111) 7x7 reconstruction geometry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT Dear colleagues, Does anyone knows where I can get a z-matrix or Cartesian coordinate for a cluster of silicon atoms three layers deep from the Si(111) 7x7 reconstructed surface? I would appreciate an experimental/ theoretical or combined reference. Is there a database that would supply surface unit cells geometries? Thank you very much. I will summarize the answers. Cherif ---------------------------------- Chérif F. Matta, Theoretical/Computational Chemist, Polanyi Research Group, Lash Miller Chemical Laboratories, Chemistry Department, University of Toronto, 80 St. George Street (Room 261), Toronto, Ontario, Canada M5S 1A1 .................................. Telephone: (416) 978 - 3625 Cellular: (416) 996 - 2444 Fax: (416) 978 - 7580 ---------------------------------- From chemistry-request@server.ccl.net Wed Jun 12 01:41:30 2002 Received: from chuma.cas.usf.edu ([131.247.209.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C5fUj09817 for ; Wed, 12 Jun 2002 01:41:30 -0400 Received: from localhost (oleynik@localhost) by chuma.cas.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id BAA26631 for ; Wed, 12 Jun 2002 01:41:29 -0400 (EDT) Date: Wed, 12 Jun 2002 01:41:29 -0400 (EDT) From: Ivan Oleynik To: chemistry@ccl.net Subject: INTEL XEON vs AMD ATHLON Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I sent email a couple days ago asking for advice re linux cluster vendors and critical configuration issues (I am going to summarize my findings after getting all the responses). It turned out that the choice of the processor is the most critical one. I had an impression from literature that Athlon MPX goes head by head with Xeon in terms of CPU speed for heavy numerics, but it is considerably less expensive. Surprisingly, I received several responses that contradict to my view. In particular, Xeon is only 5-10% more expensive, but it is more powerful since it is currently running at 2.4 GHz, has 400 MHz front bus plus 512 Kb of secondary cash as compared to 1.76 GHz, 266 MHz and 384 Kb for Athlon. Also, the newest linux kernel will provide multithreading on Xeons that could also result in substantial boost for numerical calculations. I think this is old question, but I would like to know what experts say: Is it really true that the new Xeon is superior than Athlon as far as heavy numerical calculations in cluster environment are concerned? Ivan Oleynik ------------------------------------------------------------------------ Ivan I. Oleynik E-mail : oleynik@chuma.cas.usf.edu Department of Physics University of South Florida 4202 East Fowler Avenue Tel : (813) 974-8186 Tampa, Florida 33620-5700 Fax : (813) 974-5813 ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Jun 11 21:29:47 2002 Received: from fommail.med.um.edu.my ([202.185.65.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C1Tkk07771 for ; Tue, 11 Jun 2002 21:29:46 -0400 Received: by FOM_MAIL with Internet Mail Service (5.5.2653.19) id ; Wed, 12 Jun 2002 09:44:33 +0800 Message-ID: <00E672CF9673D5119F42009027AA33C50150F6EC@FOM_MAIL> From: "Dr Sazaly's Lab" To: "'chemistry@ccl.net'" Subject: MOPAC7 Date: Wed, 12 Jun 2002 09:44:24 +0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C211B2.AE0CA3B0" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C211B2.AE0CA3B0 Content-Type: text/plain; charset="iso-8859-1" I'm new to MOPAC and tried running it but it gave me an error message about not being able to find the mkfile command. Can anyone help out? -Juraina- ------_=_NextPart_001_01C211B2.AE0CA3B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MOPAC7

  I'm new to MOPAC and tried = running it but it gave me an error message about not being able to find = the mkfile command.

  Can anyone help out?

   -Juraina-
 

------_=_NextPart_001_01C211B2.AE0CA3B0-- From chemistry-request@server.ccl.net Wed Jun 12 03:58:45 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C7wjj11567 for ; Wed, 12 Jun 2002 03:58:45 -0400 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-025 #30546) id <01KIU81M3FW00046HB@unisi.it> for chemistry@ccl.net; Wed, 12 Jun 2002 09:58:36 +0100 (MET) Received: from unisi.it (ccmaol3.chim.unisi.it [192.167.123.208]) by unisi.it (PMDF V6.0-025 #30546) with ESMTPA id <01KIU81CNEN2004AI7@unisi.it>; Wed, 12 Jun 2002 09:58:24 +0100 (MET) Date: Wed, 12 Jun 2002 09:58:15 +0200 From: "Nicolas Ferre'" Subject: Tinker: ionized vs. neutral state Sender: ferre@unisi.it To: chemistry@ccl.net Cc: Tinker Message-id: <3D06FF17.19F233BF@unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.61i [en_US] (X11; I; AIX 4.3) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: fr, en Dear CCL, In Tinker, the charged amino-acids (ASP, GLU and ARG, LYS but not HIS) are only defined in their ionized state (in the Amber force-field). Is their an automatic way to protonate the negative residues and to deprotonate the positive residues ? I still got the corresponding point charges from the web, however modifying the .xyz file (or the pdb file) would be a task ... too long ! Or maybe could you point a piece of code that can handle such manipulations/modifications of a protein structure (possibly free and not windows-based) ? Thanks in advance for any help. Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre@unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Jun 12 05:00:08 2002 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C906j12761 for ; Wed, 12 Jun 2002 05:00:07 -0400 Received: from pinar (pinar [139.179.97.99]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id LAA11281 for ; Wed, 12 Jun 2002 11:56:17 +0300 (EET DST) Date: Wed, 12 Jun 2002 12:13:40 +0300 (EET DST) From: Ulrike Salzner X-Sender: salzner@pinar To: ccl Subject: memory/G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Compouter Experts, I am trying to run a big job (1260 basis functions) on a dual 933MHz PC. The operating system is RedHat 7.2, and there is 1 GB of memory. I have not specified memory in the default route since test jobs showed that the performance decreased considerably even if much less memory was requested than the machine has. Now the number of processors is reduced to 1 by G98 due of lack of memory. Checking with the top command, G98 is supposed to use only 5.8% of the memory. Gtop (memory usage resident) shows that there are three main users of memory: l502 (59756k), httpd (54312k), and nautilus (54780k). Sum of resident sizes is 260752k. In contrast the command "free" gives: Mem total: 1027928, used: 1022784, free 5144, shared 47864, buffers 100320 cached 771980 I do not understand where the memory is. Is there a way to tune the system better? Would it be better to not use a graphical interface? Or am I doing everything wrong? Any suggestions will be greatly appreciated. Sincerely, Ulrike Salzner =================================================================== Dr. Ulrike Salzner Associate Professor Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== From chemistry-request@server.ccl.net Wed Jun 12 09:34:29 2002 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5CDYSj17592 for ; Wed, 12 Jun 2002 09:34:28 -0400 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id PAA03853 for ; Wed, 12 Jun 2002 15:34:25 +0200 (MET DST) Date: Wed, 12 Jun 2002 15:34:25 +0200 (MET DST) Message-Id: <200206121334.PAA03853@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: freeware program for windows for archive files Hi, is there any available freeware program to run (visualize) xmol archive files (in xyz format) for a windows platform ? thanks in advance Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Wed Jun 12 11:31:34 2002 Received: from addu.axelero.hu ([195.228.240.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5CFVXj19681 for ; Wed, 12 Jun 2002 11:31:34 -0400 Received: from chemaxon.com (user164.obuda.axelero.hu [195.228.88.164]) by mail02.axelero.hu (iPlanet Messaging Server 5.1 HotFix 0.6 (built Apr 26 2002)) with ESMTP id <0GXL00MQVMQVYO@mail02.axelero.hu> for chemistry@ccl.net; Wed, 12 Jun 2002 17:23:19 +0200 (MEST) Date: Wed, 12 Jun 2002 17:23:12 +0200 From: Ferenc Csizmadia Subject: Re: CCL:freeware program for windows for archive files To: sergiusz kwasniewski Cc: chemistry@ccl.net Message-id: <3D076760.7000605@chemaxon.com> Organization: ChemAxon MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7BIT X-Accept-Language: en-us, hu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.0) Gecko/20020530 References: <200206121334.PAA03853@luc.ac.be> Serge, The MarvinView application can display xyz files and other formats. It is in Java, so it also runs under Windows. You can download it at http://www.chemaxon.com/products.html Documentation: http://www.chemaxon.com/marvin/doc/mview.html This application is free for academic and home users. Best regards, Ferenc PS: You may be interested that MarvinView is also available as an applet for web applications and as a JavaBean for creating Java applications sergiusz kwasniewski wrote: >Hi, > >is there any available freeware program to run (visualize) xmol >archive files (in xyz format) for a windows platform ? > >thanks in advance > >Serge > > >___________________________________________________ > > Sergiusz Kwasniewski > LUC SBG/TS > Universitaire Campus Gebouw D > 3590 Diepenbeek > BELGIUM > > tel(direct): 032 (0)11/268315 > fax : 032 (0)11/268301 > email : sergiusz.kwasniewski@luc.ac.be > http://www.luc.ac.be/Research/TheoChem >___________________________________________________ > > >-= This is automatically added to each message by mailing script =- >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 > > > > > > > > -- Dr. Ferenc Csizmadia CEO ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T: +3620 9570988, +361 2504407 Fax: +361 2509192 mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Wed Jun 12 03:03:49 2002 Received: from alpha5.iso.port.ac.uk ([148.197.254.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C73mj10592 for ; Wed, 12 Jun 2002 03:03:48 -0400 Received: from lu07.nwservers.iso.port.ac.uk ([148.197.251.180]) by alpha5.iso.port.ac.uk with esmtp (Exim 3.22 #2) id 17I1mO-0001cw-00; Wed, 12 Jun 2002 07:38:52 +0100 Received: from LU07/SpoolDir by LU07.nwservers.iso.port.ac.uk (Mercury 1.48); 12 Jun 02 07:38:40 +0100 Received: from SpoolDir by LU07 (Mercury 1.48); 12 Jun 02 07:27:32 +0100 From: Organization: University of Portsmouth To: "EuroQSAR 2002" Date: Wed, 12 Jun 2002 07:27:28 +0100 X-Distribution: Bulk MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Subject: Registration warning - EuroQSAR 2002 Reply-to: martyn.ford@port.ac.uk CC: davel@chmqst.demon.co.uk, colin.peake@sirius-analytical.com, nicki.cordery@sirius-analytical.com, PHAJDEAR@livjm.ac.uk, han_waterbeemd@sandwich.pfizer.com, dave.pert@port.ac.uk, amy.hurst@qclscientific.com Message-ID: <3D06F8C1.3842.4C766@localhost> Priority: normal Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id g5C73nj10593 Hi, Registration for EuroQSAR 2002 All delegates who have registered for EuroQSAR 2002 should have received: Acknowledgementby e mail that their registration has been accepted and is being processed A package of information including details of hotels, the social programme and instructions for payment of registration and other fees; this should have arrived within one week of the conference organisers receiving your registration. If you think that you have registered, but have not received one or other of these responses, you should contact Nicki Cordery at Sirius Analytical Instruments by e mail AS SOON AS POSSIBLE! Nicki’s telephone number is (0)1342 820727 and her e mail address is: { HYPERLINK mailto:Nicki.cordery@sirius-analytical.com }Nicki.cordery@sirius-analytical.com You are also advised to copy your e mail to me at: { HYPERLINK mailto:martyn.ford@port.ac.uk }martyn.ford@port.ac.uk Failure to respond to this message at once could mean that you fail to qualify for a discounted rate (the deadline is Friday June 15th). Look forward to seeing you by the seaside later this summer, Best wishes, Martyn Ford Symposium Chairman From chemistry-request@server.ccl.net Wed Jun 12 03:28:56 2002 Received: from ns.ice.mpg.de ([195.37.47.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C7Suj10964 for ; Wed, 12 Jun 2002 03:28:56 -0400 Received: from relax.ice.mpg.de ([10.10.11.61] helo=ice.mpg.de) by ns.ice.mpg.de with esmtp (Exim 3.14 #17) id 17I2Yp-0005vq-00; Wed, 12 Jun 2002 09:28:55 +0200 Message-ID: <3D06F836.6010103@ice.mpg.de> Date: Wed, 12 Jun 2002 09:28:54 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.0) Gecko/20020530 X-Accept-Language: en-us, en MIME-Version: 1.0 To: FyD CC: chemistry@ccl.net, Gil.Utard@ens-lyon.fr Subject: Re: CCL:Cluster for AMBER/GAMESS/GAUSSIAN References: <20020611144513.5829F7EB1@gip.u-picardie.fr> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit FyD wrote: > Dear All, > > We are going to buy a cluster of dual athlon MP 2000+ to work with AMBER6/7, > GAMESS and GAUSSIAN. > We hesitate between - a Myrinet 2GB or a 1GB Ethernet network and > - SCSI HDs 15000 rpm/SCSI 10000 rpm or IDE 7200 rpm > > Both Myrinet 2GB and SCSI HD 15000 rpm are really more expensive but might > or might not be crucial... > Moreover, GAMESS, GAUSSIAN and AMBER might not need the same network or HDs > for optimizing calculations... > > What is crucial for AMBER (MM) and for GAMESS/GAUSSIAN (QM) ? > > Thanks to all, Kind regards, Francois My 16-Nodes linux cluster (http://www/departments/ChemInf/edda.html) runs on 100 MBit Ethernet. The Gaussian 98 calculations scale nicely (http://www/departments/ChemInf/g98scaling.html) for up to 8 nodes. Please note, that this might be true only for the B3LYP geometry optimization that we do. Due to this behaviour, I have logically splitted the cluster into two, using the PBS batch system, because we run a lot of jobs and two simultaneous jobs on 8 nodes each are much more sensible then one on 16, if you have hundreds of jobs in the queue. For us, the 100 MBit Ethernet seems to be ok. We have been convinved by others that ab-initio calculations of the type that we run always show that scaling behaviour that we see and that thus a faster network would be a waste of money. I understand that today GBit Ethernet costs as must as did the 100 MBit stuff at the time we bought our cluster, so this would be my choice. I have nothing to contribute with respect to HD speed and MM calcs :-) Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Wed Jun 12 05:04:06 2002 Received: from relay1.softcomca.com ([168.144.1.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5C946j12894 for ; Wed, 12 Jun 2002 05:04:06 -0400 Received: from m2w098.softcomca.com ([168.144.108.98]) by relay1.softcomca.com with Microsoft SMTPSVC(5.0.2195.4905); Wed, 12 Jun 2002 05:04:06 -0400 X-Originating-IP: 202.185.72.119 X-URL: http://www.mail2web.com/ Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Wed, 12 Jun 2002 05:04:06 -0400 To: "chemistry@ccl.net" Reply-To: nepenthes@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-ID: X-OriginalArrivalTime: 12 Jun 2002 09:04:06.0459 (UTC) FILETIME=[1B1E50B0:01C211F0] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id g5C946j12895 Hi CCLers, Can anybody suggest where I might find information regarding some analogues of L-arginine? I'd like to find out some structural information and if possible, pKa of the side chains of L-ornithine, L-citrulline and L-homoarginine. Thank you in advance. -Rowyna K.- -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Wed Jun 12 02:06:32 2002 Received: from web13403.mail.yahoo.com ([216.136.175.61]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g5C66Vj10171 for ; Wed, 12 Jun 2002 02:06:31 -0400 Message-ID: <20020612060627.19400.qmail@web13403.mail.yahoo.com> Received: from [128.97.147.209] by web13403.mail.yahoo.com via HTTP; Tue, 11 Jun 2002 23:06:27 PDT Date: Tue, 11 Jun 2002 23:06:27 -0700 (PDT) From: eric hu Subject: linux babel To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I wonder if anyone can point me the place to download a linux version BABEL. P.S. I searched the ccl.net website and it did not seem to give too much valuable informations. I'm sure my question could be well avoided if the text archives are a little bit more organized. Eri __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com From chemistry-request@server.ccl.net Wed Jun 12 13:22:26 2002 Received: from tomts19-srv.bellnexxia.net ([209.226.175.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5CHMQj21215 for ; Wed, 12 Jun 2002 13:22:26 -0400 Received: from Blinga ([64.231.128.189]) by tomts19-srv.bellnexxia.net (InterMail vM.5.01.04.19 201-253-122-122-119-20020516) with SMTP id <20020612172225.OHHV15871.tomts19-srv.bellnexxia.net@Blinga> for ; Wed, 12 Jun 2002 13:22:25 -0400 Message-ID: <008f01c21235$914610d0$1b02a8c0@Blinga> From: "Tim Blacker" To: Subject: New Software for Developing HTS Screens Date: Wed, 12 Jun 2002 13:21:19 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_008C_01C21214.0A0809A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_008C_01C21214.0A0809A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Pharma Algorithms, a Toronto-based software company has released = Algorithm Builder and four high-throughput ADME/Tox screens. Algorithm Builder (AB): A desktop system allowing you to build QSAR, QSPR and SAR models for = rapid hypothesis testing.=20 These models are then easily converted to rule-based algorithms for = screening new molecules.=20 This flexible system allows visual, on-screen assembly of custom = physico-chemical predictors, Lipinski-type filters and complex property = screens. Previously time-consuming tasks have been automated resulting in = substantial efficiency gains - Algorithm Builder makes manual = derivations obsolete. No programming language needs to be learned to build high quality = algorithms=20 AB features include:=20 . automated structure fragmentation (atomic, functional group, = core-scaffold), structural information matrices=20 . over 100 built-in constitutional and phys-chem descriptor calculators, = . statistical analysis (MLR, BR, PLS, PCA, kNN) as well as Recursive = Partitioning and Hierarchical Clustering analysis tools.=20 . use fragmental methods and similarity analysis in algorithms. Insert = equations and conditions with a simple parser.=20 . compiled algorithm files are easily exported and shared with = colleagues. ADME/Tox Screens: - Toxicity: acute toxicity screening based on 70,000 LD50 = values =20 - Human Intestinal Absorption (HIA): identifies compounds = with poor intestinal permeability =20 - Ionization: estimates pKa and ion form fractions at any pH =20 - Aqueous Solubility: estimates solubility of non-ionized = electrolytes in pure water =20 ADME/Tox filters provide the tools to quickly identify poor candidates.=20 These filters are provided as standalone "black-box" predictors or as = customizable "look-inside" algorithms when used as add-ins to Algorithm = Builder.=20 For more information please visit our web site, www.ap-algorithms.com, = or e-mail us: info@ap-algorithms.com =20 "The Advanced Algorithm Builder is a highly versatile and useful tool = for the bench chemist who wants to validate his working hypothesis in a = quantitative manner," Prof. Dr. Hugo Kubinyi. Professor of Pharmaceutical Chemistry at the University of Heidelberg, = Germany. Former Chair of the QSAR and Modelling Society and former head = of Drug Design at BASF AG, Germany. Tim Blacker Director of Sales, North America blacker@ap-algorithms.com=20 www.ap-algorithms.com=20 Pharma Algorithms 591 Indian Rd Toronto, ON, Canada M6P 2C4 T 416-516-3289 F 416-516-1401 ------=_NextPart_000_008C_01C21214.0A0809A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Pharma Algorithms, a = Toronto-based=20 software company has released Algorithm Builder and four=20 high-throughput ADME/Tox screens.

 

Algorithm Builder = (AB):

 

A desktop=20 system allowing you to build QSAR, QSPR and SAR models for rapid = hypothesis=20 testing.

These=20 models are then easily converted to rule-based algorithms for screening = new=20 molecules.

This=20 flexible system allows visual, on-screen assembly of custom = physico-chemical=20 predictors, Lipinski-type filters and complex property=20 screens.

Previously time-consuming tasks have been automated = resulting in=20 substantial efficiency gains - Algorithm Builder makes manual = derivations=20 obsolete.

No=20 programming language needs to be learned to build high quality=20 algorithms 

 

AB=20 features include:

 

=95 automated structure fragmentation (atomic, = functional group,=20 core-scaffold), structural information matrices

=95 over 100 built-in constitutional and phys-chem = descriptor=20 calculators,

=95 statistical analysis (MLR, = BR, PLS, PCA,=20 kNN) as well as Recursive Partitioning and Hierarchical Clustering = analysis=20 tools.

=95 use fragmental methods and = similarity=20 analysis in algorithms. Insert equations and conditions with a simple = parser.=20

=95 compiled algorithm files = are easily=20 exported and shared with colleagues.

 

 

ADME/Tox=20 Screens:

 

          =   -=20 Toxicity: acute = toxicity=20 screening based on 70,000 LD50 values

 

           =  -=20 Human Intestinal Absorption (HIA): identifies compounds = with poor=20 intestinal permeability

 

           =  -=20 Ionization: = estimates=20 pKa and ion form fractions at any pH

 

           =  -=20 Aqueous Solubility:=20 estimates solubility of non-ionized electrolytes in pure = water

 

ADME/Tox = filters=20 provide the tools to quickly identify poor candidates.

These=20 filters are provided as standalone "black-box" predictors or as=20 customizable "look-inside" algorithms when used as add-ins to = Algorithm=20 Builder.

 

 

For more information = please visit=20 our web site, www.ap-algorithms.com,=20 or e-mail us: info@ap-algorithms.com<= /P>

 

"The=20 Advanced Algorithm Builder is a highly versatile and useful tool for the = bench=20 chemist who wants to validate his working hypothesis in a=20 quantitative manner," Prof.=20 Dr. Hugo=20 Kubinyi.

Professor of Pharmaceutical Chemistry at the University = of=20 Heidelberg, Germany. Former Chair of the QSAR and Modelling Society and = former=20 head of Drug Design at BASF AG, Germany.


 Tim Blacker
 Director of = Sales, North=20 America
 
 blacker@ap-algorithms.com=20
 www.ap-algorithms.com=20
 
 Pharma Algorithms
 591 = Indian=20 Rd
 Toronto, ON, Canada
 M6P 2C4
 T=20 416-516-3289
 F 416-516-1401
------=_NextPart_000_008C_01C21214.0A0809A0--