From chemistry-request@server.ccl.net Wed Dec 6 01:55:02 2000 Received: from chem.ch.huji.ac.il (chem.ch.huji.ac.il [132.64.90.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA30650 for ; Wed, 6 Dec 2000 01:55:01 -0500 Received: from yfaat.ch.huji.ac.il (yfaat.ch.huji.ac.il [132.64.98.55]) by chem.ch.huji.ac.il (8.9.3/8.9.3) with ESMTP id IAA03598 for ; Wed, 6 Dec 2000 08:54:52 +0200 (IST) Sender: dodik@chem.ch.huji.ac.il Message-ID: <3A2DE2BC.2859625@yfaat.ch.huji.ac.il> Date: Wed, 06 Dec 2000 08:54:52 +0200 From: David Danovich Organization: Institute of Chemistry, The Hebrew University X-Mailer: Mozilla 4.5 [en] (X11; I; AIX 4.2) X-Accept-Language: ru MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: CCL: Optical rotation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL's, Which programs can I used to calculate optical rotation? Thanks David -- Dr. David Danovich, Department of Organic Chemistry, The Hebrew University, Givat-Ram Campus, 91904 Jerusalem, Israel http://yfaat.ch.huji.ac.il/david.html, dodik@yfaat.ch.huji.ac.il FAX:(+972)-2-6585345, Phone:(+972)-2-6586934(w), (+972)-2-9995935(h) From chemistry-request@server.ccl.net Wed Dec 6 09:16:37 2000 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA00875 for ; Wed, 6 Dec 2000 09:16:32 -0500 Received: from lauca.usach.cl ([158.170.51.105]) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id eB6EDbL03690; Wed, 6 Dec 2000 11:13:37 -0300 (CDT) Message-ID: <3A2E4AE1.399F3A8E@lauca.usach.cl> Date: Wed, 06 Dec 2000 11:19:14 -0300 From: Danilo Gonzalez X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, richard Subject: Summary: Protein Docking Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Thanks Sohail, Michael Meyer, and Richard Gillilan for their excelente response. Thank you very much. My previous question is: --------------------------------------------------------------------------- I'm looking for some references about the protein docking and interaction between proteins. I will appreciate if you can send me some references about this subject. -------------------------------------------------------------------------- I summarizes all the responses as follows, ******************************************************** Have a look at this site. http://www.scripps.edu/pub/olson-web/doc/autodock/references.html In addition subscribe to chemwem.Its a dreat collection of refrences. http://www.chemweb.com what method u will use for docking might be I can give u some more information. sohail university sains malaysia. *********************************************************** Dear Fernando, here are a few references. There are a lot of other interesting references cited in these papers. N. Horton, M. Lewis, Calculation of the free energy of association for protein complexes, Protein Sci. 1, 169 (1992). J. Janin, Elusive Affinities, Proteins 21, 30 (1995). J. Janin, Principles of Protein-protein recognition - from structure to thermodynamics, Biochimie 77, 497 (1995) J. Janin, F. Rodier, Protein-Protein interaction at crystal contacts, Proteins 23, 580 (1995). D. Fischer et al., A geometry-bases suite of molecular docking processes, JMB 248, 459 (1995). C.-J. Tsai et al., Protein-Protein interfaces: ..., Critical rev. Biochem. Mol. Bio. 3, 127 (1996). M. Meyer et al., Hydrogen bonding and molecular surface shape complementarity ..., JMB 264, 199 (1996). J. Otlewski, W. Apostoluk, Structural and energetical aspects of protein-protein recognition, Acta Biochimica Polonica 44, 367 (1997). N. S. Blohm, J. Sygusch, High resolution fast quantitative docking using Fourie Domain correlation techniques, Proteins 27, 493 (1997). R. M. Jackson et al., Rapid refinement if protein interfaces incorporating solvation:..., KMB 276, 265 (1998). M. J. E. Sternberg et al., Predictive docking of protein-protein and protein-DNA complexes, Curr. Opin. Struct. Biol. 8, 250 (1998). Michael -- Michael Meyer Konrad-Zuse-Zentrum Takustrasse 7 D-14195 Berlin Germany E-mail: meyer@zib.de Tel. (++49) 30/84185-327 Fax (++49) 30/84185-107 http://www.zib.de/meyer/ ********************************************************** Protein-protein interaction: J.A. McCammon "Theory of biomolecular recognition" Curr. Op. in Struct Biol. 1998 8:245-249 S. Jones and J. M. Thornton "Principles of protein-protein interaction" Proc. Natl. Acad. Sci. USA vol 93 pp 13-20 Jn 1996 J. Janin and C. Chothia "The Structure of Protein-Protein Recognition Sites" J. Biol. Chem vol 265 no 27 pp 16027-16030 1990 J. Janin, S Miller, C Cothia "Surface, Subunit Interfaces and Interior of Oligomeric Proteins" J. Mol Bio. (1988) 204 pp155-164 Docking: J. Cherfils and J. Janin "Protein docking algorithms: simulating molecular recognition" Current Opinion in Structural Biology 1993, 3:265-269 M. Sternberg, H.A. Gbb ad RM Jackson "Protein docking algorithms: simulating molecular recognition" Current opinion in Structural Biology 1998, 8:250-256 I. A. Vakser, O. G. Matar and C. F. Lam "A Systematic Study of low-resolution recognition in protein-protein complexes" PNAS vol 96 pp8477-8482 1999 D. Fischer et.al. "A Geometry-based Suite of Molecular Docking Processes" J. Mol. Bio. (1995) 248 pp459-477 FTDOCK (Gabb J. Mol Biol 272 106-120 1997) DOT (Lynn F. Ten Eyck) sorry don't have a ref for this program Also check out Bruce Duncan's Harmony program: http://www.scripps.edu/pub/olson-web/doc/harmony/harmony.html Hope this helps. Richard Gillilan MacCHESS/MBG Cornell University From chemistry-request@server.ccl.net Wed Dec 6 16:46:27 2000 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA02613 for ; Wed, 6 Dec 2000 16:46:27 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/IUPUIPO.1.3) with SMTP id QAA01767; Wed, 6 Dec 2000 16:46:25 -0500 (EST) Message-ID: Date: 6 Dec 2000 17:03:56 -0500 From: "Boyd" Subject: Combinatorial library design To: "CHMINF-L" , "MEDI ACS Listserv" , "Mol-diversity list" , "OSC CCL" , "PDB list" , "QSAR & Modelling Society" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hello All, I would like to bring attention to the latest issue of the Journal of Molecular Graphics and Modelling (Vol. 18, No. 4/5). It is a special issue on "Advances in Combinatorial Library Design" organized by Dr. Dimitris Agrafiotis (3-Dimensional Pharmaceuticals) and Dr. Eric Martin (Chiron). The articles are: Robert P. Sheridan, Sonia G. SanFeliciano, and Simon K. Kearsley, Designing targeted libraries with genetic algorithms. Paul Beroza, Erin K. Bradley, John E. Eksterowicz, Robert Feinstein, Jonathan Greene, Peter D. J. Grootenhuis, Randall M. Henne, John Mount, William A. Shirley, Andrew Smellie, Robert V. Stanton, and David C. Spellmeyer, Applications of random sampling to virtual screening of combinatorial libraries. Sarah J. Edgar, John D. Holliday and Peter Willett, Effectiveness of retrieval in similarity searches of chemical databases: A review of performance measures. Andrew R. Leach, Richard A. Bryce, and Alan J. Robinson, The synergy between combinatorial chemistry and de novo design. Dmitrii N. Rassokhin and Dimitris K. Agrafiotis, The Kolmogorov- Smirnov statistic and its applications in library design. Eric J. Martin and Thomas J. Hoeffel, Oriented substituent pharmacophores PRopErtY Space (OSPPREYS): A substituent- based calculation that describes the library products better than the corresponding product-based calculation. Robert D. Clark, David E. Patterson, Farhad Soltanshahi, James F. Blake, and James B. Matthew, Visualizing substructural fingerprints. Marvin Waldman, Hong Li, and Moises Hassan, Novel algorithms for the optimization of molecular diversity of combinatorial libraries. Robert D. Brown, Moises Hassan, and Marvin Waldman, Combinatorial library design for diversity, cost efficiency and drug-like character. Jonathan S. Mason and Brett R. Beno, Library design using BCUT chemistry-space descriptors and multiple 4-point pharmacophore fingerprints - simultaneous optimization and structure-based diversity. John M. Barnard, Geoff M. Downs, Annette von Scholley-Pfab, and Robert D. Brown. Use of Markush structure analysis techniques for SMILES and fingerprint generation and clustering large combinatorial libraries. Paul Labute, A widely applicable set of descriptors. Shenghua Shi, Zhengwei Peng, Jaroslaw Kostrowicki, Genevieve Paderes, Atsuo Kuki, Efficient combinatorial filtering for desired molecular properties of reaction products. Michael S. Siani, A. Geoffrey Skillman, Christopher W. Carreras, Gary Ashley, Irwin D. Kuntz, and Daniel V. Santi, Development and screening of a polyketide virtual library for drug leads against a motilide pharmacophore. Tudor I. Oprea, Johan Gottfries, Vladamir Shcherbukhin, Peder Svensson, and Thomas C. KŸhler, Chemical information management in drug discovery: optimizing the computational and combinatorial chemistry interfaces. Online versions of the articles are at www.chemweb.com. Thanks, Don Donald B. Boyd, Ph.D. Editor, Journal of Molecular Graphics and Modelling Member, American Chemical Society's Computers in Chemistry Division E-mail boyd@chem.iupui.edu Web http://chem.iupui.edu/~boyd/jmgm.html (Please excuse cross-posting.) From chemistry-request@server.ccl.net Wed Dec 6 17:02:22 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA02685 for ; Wed, 6 Dec 2000 17:02:22 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id RAA14139; Wed, 6 Dec 2000 17:02:21 -0500 (EST) Date: Wed, 6 Dec 2000 17:02:20 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Support CCL again -- few explanations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, It is again me with the Support CCL, Please... (Do not dare to push the d button yet...). After looking at the very well written request for support of Gordon Research Conferences in Computational Chemistry (which I support very much) and after getting several questions on the recently announced support drive for CCL, I need to pitch again (I will soon sound like your neighborhood Public Radio Station for those in the US). I really would appreciate your support for CCL. While OSC is giving CCL a lot of support, and thanks to OSC's support and encouragement the CCL will be 10 years old in January, maintaining the list and the site is labor intensive. Making it better is even more expensive, since it requires that I buy myself from other duties. So please consider helping. It does not have to be much, but every dollar helps to pay students working the list, buy hardware and software, pay the disposables and phones, etc... Your support also shows the world that you consider CCL worthy your support. You can help CCL sending small installments (if you prefer to do it this way), or just send us some money every year or so. Please scan the information on the Web at: http://www.ccl.net/chemistry/aboutccl/supporting/ and learn about details. We do not monitor the traffic to CCL pages, since we are too busy to do that. No evil script will grab your identity and put it on a "prospect e-mail list". We do not do such things... So please read what I have to say, even if you cannot contribute at this moment. You may learn a few things about the list and our mission. In short... We are educational charity, formally a part of OSU (OSC is formaly a department of OSU for accounting purposes) , so your donations to CCL are tax deductible in US (and probably in many other countries, but you know better). After donating, you will get the official thank you letter acknowledging your support which you can use for tax purposes. If you do not want to read all this and fill up forms, and you just want us to thank you in our Donor Page: http://www.ccl.net/cgi-bin/donors you can: 1) Send me a check with your donation to: OSC Development Fund (CCL) Attn. Jan K. Labanowski 1224 Kinnear Rd Columbus, OH 43212-1163, USA 2) FAX a simple page with your contact information (Name, Address, Phone) amount of donation, kind of your credit card (only Visa or MC are accepted at this moment), credit card number, expiration date, and SIGNATURE and address it to: OSC Development Fund (CCL) Attn. Jan K. Labanowski FAX: 614-688-3998 This is a secure FAX located in the closed space of OSC business office. 3) Just call me at 614-292-9279 (my OSC office) or 614-487-8373 (home office, I often telecommute {:-)} -- also my wife can write it down) and if I am there, I will gather the needed information (i.e., Credit Card information, contact, information and the amount you want to donate. Send me also e-mail (jkl@ccl.net) that you called, so I can confirm your donation immediately and have some tangible proof that you are you {:-)}. We are the same time as New Your City, and please do not call me at 4am {:-)}. DO NOT SEND ME CREDIT CARD NUMBERS BY EMAIL, PLEASE... Note we have to have your contact information even if you want to be anonymous. We will not share this information but we are required by law to know who gave us money. If you have other ideas how to support CCL financially, please do not hesitate to contact us at support@ccl.net or just call me at 614-292-9279. We are flexible and open to suggestions. I want also to thank you all of you who support CCL with your lively exchanges and discussions, you contribution to CCL archives, and the occasional pat on the back for what we are doing here. If you do not want to help us financially, please contribute in other ways, so it makes sense for us to seek financial help. Jan Labanowski Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Wed Dec 6 22:10:07 2000 Received: from fep3.online.sh.cn ([202.96.209.76]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA03965 for ; Wed, 6 Dec 2000 22:10:06 -0500 Received: from cadd ([61.129.168.61]) by fep3.online.sh.cn (InterMail vM.4.01.02.39 201-229-119-122) with SMTP id <20001207031018.BAJO477.fep3.online.sh.cn@cadd> for ; Thu, 7 Dec 2000 11:10:18 +0800 Date: Thu, 7 Dec 2000 11:12:35 +0800 From: Ji Hai-tao To: "chemistry@ccl.net" Subject: IR camptothecin Organization: School of pharmacy, second military medical university X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20001207031018.BAJO477.fep3.online.sh.cn@cadd> Dear sir, I am making research of IR properties of camptothecin by quantum chemical methods.I wonder if any of you can supply me with a picture of infrared spectrum of camptothecin? Can you tell me any free resources that includes IR spectrum? Thank you in advance! sincerely, Yun-Long Song, Ph.D. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ School of pharmacy Second military medical university 325 Guohe Road, Shanghai 200433 P. R. China e-mail: songyunlong@263.net ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~