From chemistry-request@ccl.net Tue May 26 01:55:40 1992 Date: Mon, 25 May 92 23:30:33 EDT From: PNCSPPC@ccvax1.cc.ncsu.EDU Subject: Computer-Aided Drug Design, etc.? To: CHEMISTRY@ccl.net Status: R Dear fellow netters, I am a graduate student planning to enter a Ph.D. program in medicinal chemistry. One area that I'm interested in learning more about is computer- aided drug design. Does anyone know of any lists that deal specifically with the areas of medicinal chemistry, pharmacognosy (not to be confused with pharmacology) or computer-aided drug design? Phil Calvert **************************************** * Bitnet: pncsppc@ncsuvax.bitnet * * Internet: pncsppc@ccvax1.cc.ncsu.edu * **************************************** From chemistry-request@ccl.net Tue May 26 07:35:03 1992 Date: Tue, 26 May 92 09:57 FST From: Marie-Madeleine Rohmer 88-41-61-42 Subject: address Prof. W.J. Evans (Irvine) To: chemistry@ccl.net Status: R Does anyone have a Fax number or email address of Professor William J. Evans Department of Chemistry University of California Irvine, Cal 92717 Thanks for responding Marie-Madeleine ROHMER (ROHMER at FRCCSC21.BITNET) From chemistry-request@ccl.net Tue May 26 12:12:42 1992 Date: Tue, 26 MAY 92 15:51 N From: ZUEGG@fscm1.dnet.tu-graz.ac.at Subject: Images Analysis To: CHEMISTRY@ccl.net Status: R Hi, net I was looking for some tools in multivariate regression to calculate some properties of enzyme-substrate reactions (like the Comparative Molecular Field Analysis (CoMFA) does), and I find the topic , that seems to have some useful features. Can anyone point out some publications reguarding multivariate regression in image analysis, and does anyone know, if there are any programs (or program packages or even codes) for UNIX/SGI or DOS/386 platforms available. Thanks in advance for any help in this matter. ------------------------------------------------------------------------------ Zuegg Johannes Institute for Organic Chemistry Fax : (++43) 316 811057 University of Technologie Mail: zuegg@fscm1.dnet.tu-graz.ac.at Graz, Austria ------------------------------------------------------------------------------ From chemistry-request@ccl.net Tue May 26 13:00:48 1992 Date: Tue, 26 May 92 10:28:51 CDT From: peschko@s1.msi.umn.EDU Subject: congen, and generating side chains from backbone atoms To: CHEMISTRY@ccl.net Status: R hello I was wondering if anyone out there in netland had used CONGEN to generate all of the sidechain atoms on a protein residue.. All I have is the backbone CA coordinates (X,Y,Z). There is no information about the orientation of the sidechain atoms. The proteins I have in mind are from 140-512 residues long.... What problems am I going to encounter when I try to find low energy structures off the generated residues? Also, what is the best algorithm to use for doing this (time is critical)? Ultimately I would like to generate a series of programs to do this automatically, straight out of a list of CA coordinates.... Any help on this matter would be greatly appreciated..... Thanks much... mail to Ed Peschko peschko@mermaid.micro.umn.edu From chemistry-request@ccl.net Tue May 26 14:01:28 1992 Date: Tue, 26 May 92 12:17:59 -0500 From: berkley@wubs.wustl.EDU (Berkley Shands) Subject: Benchmarks To: chemistry@ccl.net Status: R Once again, it is time for the boring old Angiotensin Converting Enzyme (ACE) series benchmark on various machines. After making some improvements to the code... Elapsed Child_CPU System_CPU Forks Ratio Chargable Comments ======= ========= ========== ===== ===== ========= ================================ 836 886 188 4 1.060 637 VAX 3520 32MB 401 267 26 3 0.666 190 IRIS 4d/20GT 16MB 270 150 7 3 0.556 100 SUN SPARCstation-2 24MB 219 124 5 3 0.566 73 IBM RS/6000-320H 32MB 197 99 11 3 0.503 68 E&S ESV M120 32MB 185 84 8 3 0.454 65 IRIS 4d/380 128MB (other loads) 118 77 32 3 0.653 52 IRIS 4d/RPC indigo 48MB 205 75 3 3 0.366 42 IBM RS/6000-550 64MB All machines except the indigo and the VAX had NFS served files. All times are in seconds. IRIS machines ran 4.0.1 (of some flavor or another). IBM machines ran AIX 3.2 GOLD. SUN machines ran 4.1.1B, and used a table lookup squareroot. E&S machines ran MIPS 2.2. VAX/VMS machines ran VMS 5.5 + POSIX 1.0 using BOTH CPUs. Constrained Search V5.0 / Receptor (V1.0+ beta) Running the 71 molecule ACE series benchmark. Uniform 4 degree rotations of 0:359 on all bonds. Molecules varied from 3 rotatable bonds to 10 rotatable bonds. This version of Constrained Search is a development and research only implementation. Searches with the scan factor set to under 1 degree take a weekend and show a significantly more detailed result. The last informally published time for the IRIS 4d/380 was 189 chargeable seconds. Child_CPU time includes ALL overhead, paging, swapping and file I/O. Longer runs have a much better Child_CPU to Chargable ratio. As always, your miles per gallon are nowhere near what the EPA says :-) Berkley Shands From chemistry-request@ccl.net Tue May 26 17:16:19 1992 Date: Tue, 26 May 92 15:39:39 -0400 From: nobody@Kodak.COM Subject: Finding others' addrersses. To: "chemistry@ccl.net"@Kodak.COM Status: R >From: NAME: Adi M. Treasurywala FUNC: Biophys. & Compu. Chem. TEL: (518)445-7042 To: "chemistry@ccl.net"@kodakr@mrgate@wpc Folks, The recent past has seen several mails aimed at finding out the e-mail addresses of others. (like EVERYTHING else it would sometimes be more useful to have the ANSWER than the QUESTION but that is another issue...). So I was indeed happy to see in a recent issue of PC WORLD that there is a way to find these out (for free!!) through a service known as a "knowbot". "To conduct a search with Knowbot, you need to know its Internet mailbox address: netaddress@nri.reston.va.us (case is important). On Compuserve, at the To: prompt, enter INTERNET: followed by the mailbox address (don't put a space after the colon). On MCI mail, address the message to NRI Directory Services, then when prompted for an E-mail system, type internet. Enter the mailbox address at teh next prompt. Since Knowbot will examine just the body of the message, enter only the name of the person you're seeking. Place it flush left on the first line. If you have more information about the person, add that data on succeeding lines." Example: Pete Jones service mcimail country FR org INRIA Names of the services are lower case countries are signified by their two letter ISO networking country codes. For a help file of Knowbot commands send a message with a question mark on the first line. I have not yet had occassion to try it out and would appreciate any experiences that anyone may have in this area. I would prefer to have answers to the net directly so that others may benefit also. (summaries of results are few and far between I find. How about others?) Adi Treasurywala. (adit@kodak.com)