From chemistry-request@ccl.net Sun Jul 20 21:14:37 2003 Received: from mailpo.embl-hamburg.de (mailpo.EMBL-Hamburg.DE [192.109.31.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6L1Eajq014713 for ; Sun, 20 Jul 2003 21:14:37 -0400 Received: from embl-hamburg.de (hanuman.EMBL-Hamburg.DE [192.109.31.90]) by mailpo.embl-hamburg.de (8.12.8/8.12.8) with ESMTP id h6L1EYbc005738; Mon, 21 Jul 2003 03:14:34 +0200 Message-ID: <3F1B3E79.4000407_at_embl-hamburg.de> Date: Mon, 21 Jul 2003 03:14:33 +0200 From: Peter Zwart User-Agent: Mozilla/5.0 (Macintosh; U; PPC Mac OS X; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Pedro Antonio Reche CC: ccp4bb_at_dl.ac.uk, chemistry_at_ccl.net Subject: Re: [ccp4bb]: modeling inhibitor in groove References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-RAVMilter-Version: 8.4.3(snapshot 20030212) (mailpo.EMBL-Hamburg.DE) X-Spam-Status: No, hits=-1.1 required=5.0 tests=QUOTED_EMAIL_TEXT,REFERENCES,USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > > Hi, I have a PDB of a kinase in complex with a inhibitor, and I would > like to replace that inhibitor with a related compound. I have > already generated a PDB file for this compound but I do not I have > to proceed, and thereby any input about the software (better if unix > open source), and strategy to replace the original inhibitor with > this related compound will be greatly appreciated. Also, does anyone > know of a software to overlay 3D structures of small molecules? I am > thinking that overlaying the derivative compound with the inhibitor > in the 3D structure of the kinase would be a possibility, but what > software to use?! > Anyway, any idea, or suggestion about best way to solve this problem > will be greatly appreciated. > Cheers You could give MOLREP a try, the manual says: ----------------------------------------------------------------------------------------------------------------- Fitting two models (FM) The idea is to fit the electron densities instead of the atomic models, trying to find the best overlap. Advantages are: * can be used for cases with very low homology; * can be used when amino acid sequence is absent; * no need to use the list of equivalent atoms. If you define only two files of models (searching model and model_2), without a file of structure factors (Fobs), the program will fit the search model (keyword FILE_M ) to the second model (keyword MODEL_2 ). The search model must be smaller or equal to the second model. ----------------------------------------------------------------------------------------------------------------- No clue how to handle (large) conformational differences though. Or soak and solve maybe ? Peter Zwart This e-mail was scanned by RAV Antivirus. (www.ravantivirus.com) From chemistry-request@ccl.net Sat Jul 19 11:27:58 2003 Received: from research.dfci.harvard.edu (research.dfci.harvard.edu [155.52.50.28]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6JFRwjq015802 for ; Sat, 19 Jul 2003 11:27:58 -0400 Received: from [155.52.22.103] (HELO research.dfci.harvard.edu) by research.dfci.harvard.edu (CommuniGate Pro SMTP 4.0.6) with ESMTP id 1060758 for chemistry:at:ccl.net; Sat, 19 Jul 2003 11:28:22 -0400 Date: Sat, 19 Jul 2003 11:27:58 -0400 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: text/plain; delsp=yes; charset=US-ASCII; format=flowed Subject: modeling inhibitor in groove From: Pedro Antonio Reche To: chemistry:at:ccl.net Content-Transfer-Encoding: 7bit Message-Id: <936E1B46-B9FD-11D7-B6E3-000393BC20D0:at:research.dfci.harvard.edu> X-Mailer: Apple Mail (2.552) Hi, I have a PDB of a kinase in complex with a inhibitor, and I would like to replace that inhibitor with a related compound. I have already generated a PDB file for this compound but I do not I have to proceed, and thereby any input about the software (better if unix open source), and strategy to replace the original inhibitor with this related compound will be greatly appreciated. Also, does anyone know of a software to overlay 3D structures of small molecules? I am thinking that overlaying the derivative compound with the inhibitor in the 3D structure of the kinase would be a possibility, but what software to use?! Anyway, any idea, or suggestion about best way to solve this problem will be greatly appreciated. Cheers ======================================================================== ====== Pedro A Reche, PhD MIF Bioinformatics Group Head Dana-Farber Cancer Institute (D1510A) TL: 617 632 3824 Harvard Medical School FX: 617 632 3351 44 Binney Street , EM: reche:at:research.dfci.harvard.edu Boston, MA 02115, USA W3: www.mifoundation.org From chemistry-request@ccl.net Sun Jul 20 06:21:40 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6KALbjq009859 for ; Sun, 20 Jul 2003 06:21:39 -0400 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id SAA03556 for ; Sun, 20 Jul 2003 18:11:19 +0800 Message-Id: <200307201011.SAA03556:at:mx1.ustc.edu.cn> Date: Sun, 20 Jul 2003 18:13:33 +0800 From: 6!Q8@W Reply-To: dxl:at:mail.ustc.edu.cn To: CCls Subject: Help: How to determine the symmetry of the orbital after stable calculation in G98? 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