From chemistry-request@server.ccl.net Thu Jan 25 00:33:27 2001 Received: from oac40.hsc.uth.tmc.edu (oac40.hsc.uth.tmc.edu [129.106.30.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0P5XQw05954 for ; Thu, 25 Jan 2001 00:33:26 -0500 Received: from uth.tmc.edu ([127.0.0.1]) by oac40.hsc.uth.tmc.edu (Netscape Messaging Server 4.15) with ESMTP id G7PE3Q00.FFQ; Wed, 24 Jan 2001 23:33:26 -0600 Disposition-Notification-To: C S Raman From: "C S Raman" To: Robert Jorissen Cc: chemistry@ccl.net Message-ID: Date: Wed, 24 Jan 2001 23:33:26 -0600 X-Mailer: Netscape Webmail MIME-Version: 1.0 Content-Language: en Subject: Re: CCL:Inhibitors of protein-protein interactions X-Accept-Language: en X-Priority: 1 (Highest) Content-Type: multipart/mixed; boundary="--f1b36c4502d74cb" This is a multi-part message in MIME format. ----f1b36c4502d74cb Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit Rob: Take a look at: REVIEWS: ^^^^^^^ McCormick, F [2000] Curr Opin Biotechnol 11(6): 593-7 Zeng J [2000] Comb Chem High Throughput Screen 3(5): 355-62 [THIS PAPER IS FROM YOUR OWN INSTITUTE] Park & Raines [2000] 18: 847-51 Huang [2000] Pharmacol Ther 86: 201-15 Chrunyk et al., [2000] Biochemistry 39: 7092-9 KEY PAPERS: ^^^^^^^^^^^ McMillan et al., [2000] Proc Natl Acad Sci USA 97:1506-11 Guo, Zhou & Pete Schultz [2000] Science 288:2042-5 Hope this gets you started! Cheers -raman _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ C. S. Raman Assistant Professor Structural Biology Center MSB 6.128 Dept Biochemistry & Molecular Biology Univ Texas - Medical School 6431 Fannin Houston, TX 77030 Tel: 713-500-6284 Fax: 713-500-0651 E-mail: c.s.raman@uth.tmc.edu http://www-bmb.med.uth.tmc.edu/programfac/Raman/Raman.html _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ ----- Original Message ----- From: Robert Jorissen Date: Wednesday, January 24, 2001 9:41 pm Subject: CCL:Inhibitors of protein-protein interactions > Hello > > I am interested in the problem of structure-based design of inhibitors > of protein-protein interactions. This is a more difficult problem than > using the structure-based design of enzyme inhibitors since there > generally is not a deep binding pocket as there usually is in an > enzyme. > I would appreciate it if someone could tell me who are the main > researchers in this field (so that I can read some of their > papers) and > if there are any good reviews of the field. > > Thank you > > Rob > > > ----------------------------------------------------- > Robert Jorissen > > Ludwig Institute for Cancer Research > P.O. BOX 2008, Royal Melbourne Hospital > Parkville, Victoria 3050, Australia > > phone: ++61-3-9341-3155 > fax: ++61-3-9341-3104 > > e-mail: Robert.Jorissen@ludwig.edu.au > > ----------------------------------------------------- > > -= 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 > > > > > ----f1b36c4502d74cb Content-Type: text/x-vcard; name="craman.vcf"; charset=us-ascii Content-Disposition: attachment; filename="craman.vcf Content-Description: Card for C S Raman Content-Transfer-Encoding: 7bit begin:vcard n:Raman;C.S. fn:C.S. Raman tel;fax:713-500-0651 tel;work:713-500-6284 url:www-bmb.med.uth.tmc.edu/programfac/Raman/Raman.html org:University of Texas - Medical School;Biochemistry & Molecular Biology adr:;;6431 Fannin;Houston;TX;77054;U.S.A. version:2.1 email;internet:c.s.raman@uth.tmc.edu title:Assistant Professor end:vcard ----f1b36c4502d74cb-- From chemistry-request@server.ccl.net Thu Jan 25 04:54:29 2001 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0P9sSw07073 for ; Thu, 25 Jan 2001 04:54:29 -0500 Received: from zisp0203.unizh.ch (zisp0203.unizh.ch [130.60.7.159]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id KAA07096; Thu, 25 Jan 2001 10:54:28 +0100 (MET) Received: (from toukie@localhost) by zisp0203.unizh.ch (AIX4.3/8.9.3/8.8.8) id KAA06916; Thu, 25 Jan 2001 10:54:27 +0100 From: "Dr. S. Shapiro" Message-Id: <200101250954.KAA06916@zisp0203.unizh.ch> Subject: CCL:IR halfband widths (fwd) To: chemistry@server.ccl.net Date: Thu, 25 Jan 2001 10:54:27 +0100 (MET) Cc: toukie@zui.unizh.ch X-Mailer: ELM [version 2.4 PL25 PGP2] Content-Type: text Dear Colleagues; This past October I addressed a question to the CCL, but the response was underwhelming, which is to say no one responded. So I take the liberty of reposting this query in case some subscribers to this list may wish to take another crack at it. As usual, thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch Forwarded message: > From owner-chemistry@server.ccl.net Tue Oct 3 17:30:16 2000 > Message-Id: <4.3.2.7.0.20001003150508.00a85150@ziaix-imap.unizh.ch> > X-Sender: toukie@ziaix-imap.unizh.ch (Unverified) > X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 > Date: Tue, 03 Oct 2000 15:12:18 +0100 > To: chemistry@server.ccl.net > From: "Hr. Dr. S. Shapiro" > Subject: CCL:IR halfband widths > Cc: toukie@zui.unizh.ch > Mime-Version: 1.0 > Content-Type: text/plain; charset="us-ascii"; format=flowed > Sender: "Computational Chemistry List" > Errors-To: chemistry-request@ccl.net > Precedence: bulk > > Dear Colleagues; > > I quote from an article published in Spectrochim. Acta 19: 1013 (1963): > > "Band broadening can also result where a complex polyatomic molecule can > exist in different conformational forms. If the centers of conformational > isomerism are ultimately involved in the normal vibration responsible for > the absorption, it is likely that two separate bands will be resolved, and > many cases of this kind are known. However, if centers of conformational > isomerism are more remote from the atoms primarily involved in the normal > vibration, the perturbation of the steric change on the band frequency may > be very small, in which case it will only act to broaden the band. NO > EXAMPLES OF SUCH AN EFFECT HAVE YET BEEN POSITIVELY DEMONSTRATED > >...." [Emphasis by capitalisation added.] > > I would be very interested in hearing from anyone who can supply me with > references definitively demonstrating conformational IR band broadening of > the type that, as of 1963, still had not been positively demonstrated. > > Thanks in advance to all responders, > > S. Shapiro > toukie@zui.unizh.ch > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Thu Jan 25 06:34:27 2001 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0PBYQw07241 for ; Thu, 25 Jan 2001 06:34:26 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id NAA26629; Thu, 25 Jan 2001 13:33:09 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Thu, 25 Jan 2001 13:33:09 +0200 (EET) From: Mikael Johansson X-Sender: To: Roger Hull cc: Subject: Re: CCL:Autodock on Microsoft Windows platform In-Reply-To: <0+DzMGAcn2b6EwNq@mooncott.demon.co.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Roger and All! On Wed, 24 Jan 2001, Roger Hull wrote: > Has anyone tried compiling Autodock for Microsoft Windows (NT, 98, 2000, > etc.) ? (Or do you know of anyone who has ?) I have been looking at > doing so for Autodock version 3 using UWIN (a UNIX emulator for > Windows). Yes, I did compile Autodock 3.0.5 for Windows (98) using djgpp, http://www.delorie.com/djgpp/ , almost without (additional) problems. IIRC the only thing that had to be changed was to remove the file lock code. I did this as I wanted to see if a core dump I got was system specific. The scripts in the Autodock package however use a whole range of different shells, which might make their transfer to windows quite cumbersome. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry http://www.chem.helsinki.fi/ From chemistry-request@server.ccl.net Thu Jan 25 13:44:40 2001 Received: from web12201.mail.yahoo.com (web12201.mail.yahoo.com [216.136.173.85]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0PIidw10391 for ; Thu, 25 Jan 2001 13:44:40 -0500 Message-ID: <20010125184439.27373.qmail@web12201.mail.yahoo.com> Received: from [203.200.129.166] by web12201.mail.yahoo.com; Thu, 25 Jan 2001 10:44:39 PST Date: Thu, 25 Jan 2001 10:44:39 -0800 (PST) From: Bing wong Subject: g98-enough disk-semi direct : help wanted To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, I am a graduate student and new to Gaussian. I am running a # QCISD(T,E4T)/6-311G(d,p) calculation as a part of G2. The details are %MEM=240MB %CHK=TEST.chk %RWF=F1,2GB,F2,2GB,F3,2GB,F4,2GB,F5,2GB,F6,2GB Default route: MaxDisk=12GB -------------------------- # QCISD(T,E4T)/6-311G(d,p) -------------------------- on a PC pentium AMD-cpu available memory 256 MB available diskspace 18GB The message from calcultion is Range of M.O.s used for correlation: 9 146 NBasis= 146 NAE= 22 NBE= 22 NFC= 8 NFV= 0 NROrb= 138 NOA= 14 NOB= 14 NVA= 124 NVB= 124 Estimate disk for full transformation 297041010 words. Semi-Direct transformation. ModeAB= 4 MOrb= 138 LenV= 30958743 LASXX= 38419516 LTotXX= 53557291 LenRXX= 62406562 LTotAB= 8849271 MaxLAS= 75567489 LenRXY= 0 NonZer= 85688303 LenScr= 159491198 LnRSAI= 150047676 LnScr1= 256030257 MaxDsk= 1610612736 Total= 627975693 SrtSym= T ITran= 5 JobTyp=0 Pass 1: I= 1 to 138. writwa The occupancies of rwf files are F1.rwf 2,097,172KB F2.rwf 2,097,216KB F3.rwf 731,204KB As I understand the disk space requirements are less than the available. Still this calculation failed. Can anyone tell me why? and how to rectify the problem? Thank you very much. Please reply to me at wong_1977@yahoo.com Bing Wong ---------------------- __________________________________________________ Do You Yahoo!? Yahoo! Auctions - Buy the things you want at great prices. http://auctions.yahoo.com/ From chemistry-request@server.ccl.net Thu Jan 25 18:34:39 2001 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0PNYcw12119 for ; Thu, 25 Jan 2001 18:34:38 -0500 Received: from localhost (renxiao@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id PAA15144 for ; Thu, 25 Jan 2001 15:34:39 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: renxiao owned process doing -bs Date: Thu, 25 Jan 2001 15:34:39 -0800 (PST) From: Renxiao Wang To: "Dr. Renxiao Wang" Subject: Solvate organic molecules? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, For some reasons we need to solvate organic molecules or even proteins with explicit water molecules. Will anybody recommend a reliable algorithm for doing this? It will be ideal if it is able to reproduce the 'real' situations. The first layer of water is enough. Please note that we prefer an algorithm rather than a certain program. It is simply because we are writing programs in our approach. We certainly know about some programs, such as AMBER and CHARMm, which can place waters around a given molecule. But we are a little bit skeptical for what they generate on the screen. We will put back the summary if anyone else share the same interest. Regards, Renxiao Wang