Re: CCL:mutant proteins....



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<<at>>ccl.net
 
Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<<at>>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<<at>>nd.edu (read about it on CCL Home
 Page)
 
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- +-+