From chemistry-request@ccl.net Mon Dec 22 02:29:58 2003 Received: from collapsed.wormhole.hu (collapsed.wormhole.hu [195.70.35.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBM7TQHt021565 for ; Mon, 22 Dec 2003 02:29:26 -0500 Received: from szilva (helo=localhost) by collapsed.wormhole.hu with local-esmtp (Exim 3.36 #1 (Debian)) id 1AYKVG-0002Ir-00; Mon, 22 Dec 2003 08:29:22 +0100 Date: Mon, 22 Dec 2003 08:29:22 +0100 (CET) From: szilva!at!computer.org X-X-Sender: szilva!at!collapsed.wormhole.hu To: Sivanesan Dakshanamurthy cc: chemistry!at!ccl.net Subject: Re: CCL:FlexX Docking In-Reply-To: <463fe45b23.45b23463fe!at!imap.georgetown.edu> Message-ID: References: <463fe45b23.45b23463fe!at!imap.georgetown.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Szilveszter JUHOS X-Spam-Status: No, hits=-1.7 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,NO_REAL_NAME,QUOTED_EMAIL_TEXT, REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Sun, 21 Dec 2003, Sivanesan Dakshanamurthy wrote: > Could anybody explain the reason, why docking may not be able to > reproduce the native ligand in the thier structure. Hello, scoring fucntions are experimental (heuristic) functions - therefore they are only approximations. You need approximations since you want to dock libraries with numerous ligands. Somebody asked recently why do we need different scoring funcions: simply because they are different sort of approximations. If you can get the native ligand as a first from a random library then you are very lucky. Usually native ligands are in the top 1% or 5% (or ranked even worse) but rarely are the very first. You need special pre- and post-filtering procedures to get a reasonable hit library with docking. Unfortunatelly the CLL arhive search is not working, I sent these references already: M. Stahl & M. Rarey: Detailed Analysis of Scoring Functions for Virtual Screening J. Med. Chem. 2001, 44, 1035-1042 C. Bissantz, G. Folkers, and D. Rognan: Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations J. Med. Chem. 2000, 43, 4759-4767 Also the Glide tech note is very useful: http://www.schrodinger.com/docs/fd2_2002_2/pdf/fd25_technical_notes.pdf (it is analysing only one docking platform but with many targets, check the "Database enrichment" section). Cheers: Szilva From chemistry-request@ccl.net Mon Dec 22 04:08:58 2003 Received: from postfix3-2.free.fr (postfix3-2.free.fr [213.228.0.169]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBM98OHt027960 for ; Mon, 22 Dec 2003 04:08:25 -0500 Received: from linux (lns-p19-1-82-65-44-9.adsl.proxad.net [82.65.44.9]) by postfix3-2.free.fr (Postfix) with ESMTP id 6DA73C267; Mon, 22 Dec 2003 10:08:17 +0100 (CET) Content-Type: text/plain; charset="iso-8859-1" From: Konrad Hinsen Organization: CNRS To: Alex Sutcliffe , chemistry$at$ccl.net Subject: Re: CCL:rebuilding a molecule after changing the coordinates of a subsection Date: Mon, 22 Dec 2003 10:09:36 +0100 User-Agent: KMail/1.4.3 References: <3FE628C1.5080604$at$iprimus.com.au> In-Reply-To: <3FE628C1.5080604$at$iprimus.com.au> MIME-Version: 1.0 Message-Id: <200312221009.36351.hinsen$at$cnrs-orleans.fr> X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_UNCONFIRMED_DSBL,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hBM98xHt027974 On Monday 22 December 2003 00:12, Alex Sutcliffe wrote: > I have a molecule in pdb format. I have chopped out a fragment and tried > docking it to another molecule. So now I have new coordinates for just > the subsection. I would like to be able to rebuild the rest of the > molecule in relation to the new coordinates. Any suggestions on the best > way to do this? Assuming that the subsection hasn't been overly deformed in the docking process, I'd try this: Do a least-squares superposition of the subsection > from the initial to the modified conformation. Apply the resulting rigid-body transformation to the rest of the molecule. Put the two pieces together again and do some energy minimization to get a presentable molecule. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen$at$cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@ccl.net Mon Dec 22 02:36:51 2003 Received: from collapsed.wormhole.hu (collapsed.wormhole.hu [195.70.35.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBM7aKHt021999 for ; Mon, 22 Dec 2003 02:36:20 -0500 Received: from szilva (helo=localhost) by collapsed.wormhole.hu with local-esmtp (Exim 3.36 #1 (Debian)) id 1AYKbu-0002J8-00; Mon, 22 Dec 2003 08:36:14 +0100 Date: Mon, 22 Dec 2003 08:36:14 +0100 (CET) From: szilva{at}computer.org X-X-Sender: szilva{at}collapsed.wormhole.hu To: Alex Sutcliffe cc: chemistry{at}ccl.net Subject: Re: CCL:rebuilding a molecule after changing the coordinates of a subsection In-Reply-To: <3FE628C1.5080604{at}iprimus.com.au> Message-ID: References: <3FE628C1.5080604{at}iprimus.com.au> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Szilveszter JUHOS X-Spam-Status: No, hits=-1.2 required=7.0 tests=IN_REP_TO,NO_REAL_NAME,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > I would like to be able to rebuild the rest of the > molecule in relation to the new coordinates. Any suggestions on the best > way to do this? AFAIK Swiss-PDB can superpose your proteins: http://us.expasy.org/spdbv/text/toolmenu.htm or the commercial tool MOE. There are many other software I had never used for superposition. Szilva From chemistry-request@ccl.net Mon Dec 22 13:28:19 2003 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBMIRlHt015264 for ; Mon, 22 Dec 2003 13:27:48 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id hBMIRHEW018578; Mon, 22 Dec 2003 13:27:17 -0500 Date: Mon, 22 Dec 2003 13:27:17 -0500 (EST) From: Jan Labanowski To: chemistry-.at.-ccl.net cc: Jan Labanowski , Mooney-.at.-ICDD.Com Subject: Workshops on X-ray Diffraction Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ---------- Forwarded message ---------- Date: Mon, 22 Dec 2003 12:57:19 -0500 From: Leah Mooney To: Computational Chemistry List Subject: Request to Post Educational Programs Practical X-ray Fluorescence 26-30 April 2004 Sponsored by the International Centre for Diffraction Data Web: http://www.icdd.com/education E-mail: clinics-.at.-icdd.com Fundamentals of X-ray Powder Diffraction 7-11 June 2004 Sponsored by the International Centre for Diffraction Data Web: http://www.icdd.com/education E-mail: clinics-.at.-icdd.com Advanced Methods in X-ray Powder Diffraction 14-18 June 2004 Sponsored by the International Centre for Diffraction Data Web: http://www.icdd.com/education E-mail: clinics-.at.-icdd.com Thank You, Leah ******************************************** Leah Mooney Education Coordinator ICDD 12 Campus Boulevard Newtown Square, PA 19073 U.S.A. Tel: 610-325-9814 Fax: 610-325-9823 Join us on Hilton Head Island,SC for PPXRD! www.icdd.com/ppxrd From chemistry-request@ccl.net Mon Dec 22 12:02:41 2003 Received: from dft.rutgers.edu (dft.rutgers.edu [128.6.71.63]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBMH29Ht013491 for ; Mon, 22 Dec 2003 12:02:09 -0500 Received: from dft.rutgers.edu (localhost [127.0.0.1]) by dft.rutgers.edu (8.12.6/8.12.6) with ESMTP id hBMH29mP000730; Mon, 22 Dec 2003 12:02:09 -0500 Received: from localhost (kieron@localhost) by dft.rutgers.edu (8.12.6/8.12.6/Submit) with ESMTP id hBMH298n000727; Mon, 22 Dec 2003 12:02:09 -0500 Date: Mon, 22 Dec 2003 12:02:09 -0500 (EST) From: Kieron Burke To: chemistry-.at.-ccl.net cc: "Ullrich, Carsten" , Giovanni Vignale Subject: Santa Fe summer school in TDDFT, June 5-10, 2004 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Time-dependent density-functional theory (TDDFT) was established 20 years ago, and has since then made significant formal and practical progress. 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Biology Rutgers University 610 Taylor Rd, Piscataway, NJ 08854 Telephone: (732)445-1785 (office),-2618 (dept),-5312 (Fax) kieron-.at.-dft.rutgers.edu http://dft.rutgers.edu Fall 03: Mon+Wed Princeton Materials Inst. (609)258-7480