** 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
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