From chemistry-request /at\server.ccl.net Wed Feb 20 04:37:48 2002 Received: from mx04.nexgo.de ([151.189.8.80]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1K9bj518854 for ; Wed, 20 Feb 2002 04:37:46 -0500 Received: from [192.168.1.1] (dialin-212-144-143-251.arcor-ip.net [212.144.143.251]) by mx04.nexgo.de (Postfix) with ESMTP id 19E9037C06; Wed, 20 Feb 2002 10:37:06 +0100 (CET) Mime-Version: 1.0 X-Sender: (Unverified) Message-Id: In-Reply-To: References: Date: Wed, 20 Feb 2002 10:37:06 +0100 To: "nepenthes:~at~:vplaces.net" From: Thomas =?iso-8859-1?Q?H=FCbner?= Subject: Re: CCL:starting structure for docking Cc: chemistry[ AT ]ccl.net Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g1K9bm518857 Dear Rowyna, in principle your approach to take the the structure from a complex, minimize it and start your docking calculations is justifiable. Of course by using this structure and its conformation you introduce a bias, that maybe useful or dangerous, depending on the docking algorithm and the protein, which you are going to dock into. The concerns of your colleague are legitimate as well. Even if the minimization may take care of any strange bond lengths, angles and torsions, the ligand structures that you extract from protein complexes out of PDB may be too distorted for the modelling program to even extract the correct covalent structure in the first place. In that case a pure molecular mechanics minimization would not help. So in practice it is often more convenient and saver to start with a molecule builder from scratch, and, if you would like to introduce the conformational bias that I mentioned above, force it onto the conformation of the bound ligand. Yours Thomas >Dear CCLers, > >I hope you will bear with this question of mine but I wasn't able to agree with my colleague about it. I've docking a molecule, citrulline, to a protein and I obtained the citrulline molecule from a protein-citrulline complex from the PDB database website. I think it's suitable by just extracting the citrulline sequence and adding hydrogen to it and minimized the structure later on before I start my docking process. >My colleague, however, doesn't think it's an appropriate way of getting a starting structure for docking and I should use a structure from a molecule database (i.e. the cambridge crystallographic database or etc). He says that maybe the starting structure I have used may not be correct in terms of bond lengths/angle or the torsions. I don't think that is the case, since I minimized the structure anyway, so it wouldn't be any major difference if i take it from a complex structure or if I build the structure from scratch (like using the Biopolymer module from InsightII) or if I obtained it as a single molecule from a database. >I'm do apologize if this sounds very trivial but I would be grateful for some clarification as I know most of you will have experience in such matters. > >Thank you for your time. > >Rowyna K. > -- .. Dr. Thomas Hübner T2-Consult, München Phone: +49 (89) 21 58 16 80 Fax: +49 (89) 21 58 16 82 thuebner- at -t2-consult.de http://www.t2-consult.de