From chemistry-request@ccl.net Thu Jul 17 11:56:03 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6HFu3jq032329 for ; Thu, 17 Jul 2003 11:56:03 -0400 Received: from cornell.edu (wing.ccmr.cornell.edu [128.84.241.85]) by cornell.edu (8.9.3p2/8.9.3) with ESMTP id LAA21766 for ; Thu, 17 Jul 2003 11:56:01 -0400 (EDT) Message-ID: <3F16C712.4060905|at|cornell.edu> Date: Thu, 17 Jul 2003 11:56:02 -0400 From: Connie Chang User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2) Gecko/20021203 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY|at|ccl.net Subject: CCL:`Long range Coulomb forces in PM3 semiempirical methods? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi -- I was wondering if anyone out there knew if the PM3 semiempirical method includes long range Coloumbic forces? Thanks! Connie Chang From chemistry-request@ccl.net Wed Jul 16 15:07:20 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6GJ7Kjq027756 for ; Wed, 16 Jul 2003 15:07:20 -0400 Received: from cornell.edu (wing.ccmr.cornell.edu [128.84.241.85]) by cornell.edu (8.9.3p2/8.9.3) with ESMTP id PAA10634 for ; Wed, 16 Jul 2003 15:07:20 -0400 (EDT) Message-ID: <3F15A267.5020905$at$cornell.edu> Date: Wed, 16 Jul 2003 15:07:19 -0400 From: Connie Chang User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2) Gecko/20021203 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: Long range Coloumb forces included in PM3 semiempirical methods? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi -- Does anyone know if long range Coloumb forces are included in semi-empirical methods like PM3? Thanks, Connie From chemistry-request@ccl.net Wed Jul 16 15:40:51 2003 Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6GJepjq028914 for ; Wed, 16 Jul 2003 15:40:51 -0400 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7+Sun/8.11.7/NAS-6n) with ESMTP id h6GJels25181; Wed, 16 Jul 2003 12:40:47 -0700 (PDT) Date: Wed, 16 Jul 2003 12:40:47 -0700 (PDT) From: Ioana Cozmuta To: Computational Chemistry List cc: Joe M Leonard , Ioana Subject: Re: CCL:Modeling book suitable for med-chemists/overview (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am not sure what exactly you mean by modeling, I assume that you are refering to molecular (quantum or atomistic scale) modeling. I hope the following suggestions will be at least partly of help: 1. "Computational biochemistry and biophysics" edited by Oren M Becker, Al. D. MacKerell JR, Benoit Roux, Masakatsu Watanabe, Marcel Dekker Inc, 2001 2. I would look for review articles in Nature, Science. 3. There are a few review articles by Tamar Schlick that you should be able to find via the web. There are others as well, I just mention her name as I recently read a couple of her review articles. 4. Another good place to search into is http://www.phc.vcu.edu/CoolSites/link/journals.html 5. I've also tried to use on Google the search words: modeling medicinal chemistry and some good links to start with are: http://www.albmolecular.com/features/links/mmcclnx.shtml http://www.phc.vcu.edu/othercoolsites.html http://www.pharmacy.unc.edu/pharmacy/divisions/medChem/research_tropsha.html 6. You may also want to look at http://www.accelrys.com/ Good luck, Ioana On Wed, 16 Jul 2003, Joe M Leonard wrote: > Folks, > > Can anybody recommend a book (or multiple books) which would > give medicinal chemists a good overview of what modeling is > and what it might do for them? I'm not interested in one > which describes the methodology - I've got these, and the > equation count or implementation details seem intimidating. > I'd prefer something which discusses the various areas modeling's > been applied to and how it might impact their work. > > I did a quick search of "book modeling medicinal" on CCL's > archives, and didn't get anything. Any suggestions as to books > and/or places where I might find/search such things are welcome. > I would think somebody's surveyed this, either for a course or > for training/exposing med-chemists... > > Suggestions anybody? > > Thanks in advance! > > Joe Leonard > jle$at$theworld.com > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY$at$ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl$at$ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jul 17 11:18:57 2003 Received: from mx3.trentu.ca (mx3.trentu.ca [192.75.12.4]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h6HFIujq030592 for ; Thu, 17 Jul 2003 11:18:57 -0400 Received: (qmail 5916 invoked by uid 504); 17 Jul 2003 15:18:55 -0000 Received: from elewars$at$trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.16 ( Clear:. Processed in 0.028242 secs); 17 Jul 2003 15:18:55 -0000 X-Qmail-Scanner-Mail-From: elewars$at$trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.16 (Clear:. Processed in 0.028242 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx3.trentu.ca with SMTP; 17 Jul 2003 15:18:55 -0000 Message-ID: <3F16BF1B.3EB0D531$at$trentu.ca> Date: Thu, 17 Jul 2003 11:22:03 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Joe M Leonard , chemistry$at$ccl.net Subject: Re: CCL:Modeling book suitable for med-chemists/overview References: <200307161840.OAA16164$at$world.std.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 July 17 Hello, You might look at: 1) The series "Reviews in Computational Chemistry", by Lipkowitz and Boyd"; you can scan the chapter titles online. 2) A. K. Rappe and C. J. Casewit, "Molecular Mechanics Across Chemistry", University Science Books, 1997. Lots of drug applications. 3) H-D Holtje and G. Folker, "Molecular MOdelling", VCH, 1997. Goes easy on more "technical" stuff, oriented to e.g. drug design. 4) Chapter 17 in T. J. Zielinsky and M. L. Swift, "Using Computers in Chemistry and Chemical Education", ACS, 1997. 5) J. J. Vinter and M. Gardner, "Molecular Modelling and Drug Design", Macmillan, 1994. 6) Review of book in JACS, 1998, 120, 8969. 7) Review of book in JACS, 2000, 122, 3982 8) Review of book in JACS, 2000, 122, 7152 Regards, E. Lewars ============= Joe M Leonard wrote: > Folks, > > Can anybody recommend a book (or multiple books) which would > give medicinal chemists a good overview of what modeling is > and what it might do for them? I'm not interested in one > which describes the methodology - I've got these, and the > equation count or implementation details seem intimidating. > I'd prefer something which discusses the various areas modeling's > been applied to and how it might impact their work. > > I did a quick search of "book modeling medicinal" on CCL's > archives, and didn't get anything. Any suggestions as to books > and/or places where I might find/search such things are welcome. > I would think somebody's surveyed this, either for a course or > for training/exposing med-chemists... > > Suggestions anybody? > > Thanks in advance! > > Joe Leonard > jle$at$theworld.com > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY$at$ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl$at$ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Jul 17 17:11:38 2003 Received: from jilau1.Colorado.EDU (jilau1.Colorado.EDU [128.138.140.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6HLBbjq007793 for ; Thu, 17 Jul 2003 17:11:38 -0400 Received: from localhost (jilau1.Colorado.EDU [128.138.140.5]) by jilau1.Colorado.EDU (8.12.9/8.12.9/UnixOps+Hesiod) with ESMTP id h6HLBbkZ300407; Thu, 17 Jul 2003 15:11:37 -0600 (MDT) Subject: Re: CCL:Modeling book suitable for med-chemists/overview From: The Matt To: Joe M Leonard Cc: "chemistry{at}ccl.net" In-Reply-To: <200307161840.OAA16164{at}world.std.com> References: <200307161840.OAA16164{at}world.std.com> Content-Type: text/plain Organization: JILA Message-Id: <1058476297.31049.11.camel{at}ixion.colorado.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.3 (1.4.3-3) Date: 17 Jul 2003 15:11:37 -0600 Content-Transfer-Encoding: 7bit On Wed, 2003-07-16 at 12:40, Joe M Leonard wrote: > Folks, > > Can anybody recommend a book (or multiple books) which would > give medicinal chemists a good overview of what modeling is > and what it might do for them? I'm not interested in one > which describes the methodology - I've got these, and the > equation count or implementation details seem intimidating. > I'd prefer something which discusses the various areas modeling's > been applied to and how it might impact their work. > > I did a quick search of "book modeling medicinal" on CCL's > archives, and didn't get anything. Any suggestions as to books > and/or places where I might find/search such things are welcome. > I would think somebody's surveyed this, either for a course or > for training/exposing med-chemists... > > Suggestions anybody? An additional book that might be useful is "Quantum Medicinal Chemistry", edited by Paolo Carloni and Frank Alber, WILEY-VCH Verlag GmbH & Co., 2003. The only reason I know of it is that I decided to check it out and see how quantum chemical methods are used in medicine. There are lots of examples about things I have no idea about (i.e., my non-existent bio background doesn't help)[1]. HTH, Matt Thompson [1] You know, a section entitled "The Case Study: Herpes Simplex Virus Type 1 Thymidine Kinase Substrates and Inhibitors" in a QChem book is quite a bit different than what I'm used to. -- "And isn't sanity really just a one-trick pony, anyway? I mean, all you get is one trick, rational thinking, but when you're good and crazy, ooh ooh ooh, the sky's the limit!" -- The Tick The Matt -- http://ucsub.colorado.edu/~thompsma/