From chemistry-request@ccl.net Wed Sep 29 07:42:15 2004 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8TCgDGO009367 for >ccl.net>; Wed, 29 Sep 2004 07:42:14 -0500 Received: from [207.212.109.155] (p207-212-109-155.goldrush.com [207.212.109.155]) by smtp.goldrush.com (8.12.8/8.12.8) with ESMTP id i8TCqj98014418; Wed, 29 Sep 2004 05:52:48 -0700 In-Reply-To: >MAINCF1P.cf.ac.uk> References: >MAINCF1P.cf.ac.uk> Mime-Version: 1.0 (Apple Message framework v609) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <317CB74E-1216-11D9-9801-000393D4953A<>goldrush.com> Content-Transfer-Encoding: 7bit Cc: >ccl.net> From: Stephen Bowlus >goldrush.com> Subject: Re: CCL:mutant proteins.... Date: Wed, 29 Sep 2004 05:50:51 -0700 To: "Dimitrios Vlachakis" >cardiff.ac.uk> X-Mailer: Apple Mail (2.609) X-MailScanner: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: chezbowlus<>goldrush.com X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net A free minimizer for proteins is TINKER from the Jay Ponder group at WashU. It has among others an AMBER FF (or should I say a Kollman FF?) implementation, with several of the published parameter sets. Beware: The translation from the working TINKER xyz format back to a fully informative pdb format can be painful if you have limited scripting skills. Steve Bowlus On Sep 28, 2004, at 2:55 PM, Dimitrios Vlachakis wrote: > ** High Priority ** > > Dear Holly, > > first of all I will asume that you are looking for some freeware. The > most user > friendly (in terms of installation and actually using the software is > the Deep > View > Swiss-PdbViewer. It runs for all major platforms (mac 9&10, windows, > linux and > iris) and installing it just involves hitting the Ok button a few > times. All you > have to do then is to load your protein.pdb file, select the amino > acid you want > to mutate and mutate to another on from a list (all with the mouse). > > The software can be found here: > http://www.expasy.org/spdbv/ > And a tutorial on protein mutation here: > http://www.expasy.org/spdbv/text/mutation.htm > > > A quick comment though: I do not think it is very wise to do mutate > amino acids > in a protein using freeware. And there is nothing wrong with freeware, > but it is > not up to the job (most of the times). Mutating an amino acid with any > piece of > software involves the substitution of the original side chain of the > aa with the > one of the new aa. That is quite easy to do and is the easiest part of > the whole > mutation job. The problem is how viable and realistic and mutant > protein is. The > only way to fix that is to minimise energetically the protein, so that > the > energy will drop and the protein will adopt a more stable > conformation. Now, > doing that with freeware is simply IMPOSSIBLE! Deep View has > implemented a > minimisation algorithm, but it is very poor especailly when dealing > with > proteins. It uses the GROMOS 43B1 force field that is only good enough > to make > room for new (potentially larger) amino acids. So, it will get stuck > in a local > minima as it it will not be able to by pass through high energy > barriers. So, i > suggest, that you should either get your hands on a decent software > package that > can do both mutating and minimising in a proper scientific way (such > as Sybyl, > Moe, hyperchem etc) or if you are going to use freeware to do the > mutating part > (such as Deep Blue) find a reliable minimising package. a 30 day > evaluation of > hyperchem is available from here: (http://www.hyper.com) > > Hope that helps, > > > > > Dimitrios Vlachakis > PhD student in Molecular Modelling > Medicinal Chemistry Group > Welsh School of Pharmacy > Cardiff University > > Redwood Building > King Edward VII Avenue > CF10 3XF > Cardiff > Wales, UK > > tel. +44 2920 877221 > tel. +44 2920 874551 (lab) > fax. +44 2920 874537 > >> ...................................................................... >> ............. > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY<>ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST<>ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow<>nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > >