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Mutagenesis and modeling

Thomas hamelryck thomas at ultr5.vub.ac.be
Mon Feb 24 16:18:55 EST 1997

Ira Ropson (iropson at bcmic.hmc.psu.edu) wrote:
: Hello world,

: I have made several single amino acid substitutions using site-directed
: mutagenesis for a protein for which a good crystal structure is
: available. I would like to use molecular modeling techniques to compare
: the relative stability of these proteins in silico to the measurements
: I have made in vitro using denaturants. Several of these measured
: stabilities have been unexpected given the structural location and
: relative hydrophobicity of the substitutions I made. I suspect that
: simple intuition is not sufficient to explain the results, and I need
: to do some molecular modeling/molecular dynamics calculations to make
: sense of these numbers. Is this a practical idea? How should I go about
: it? Are there any reviews that are focused on this issue? How
: successful have these kinds of predictions been in the past? Is there
: any particuIar software packages that would be very useful for this
: purpose? I currently have a Silicon Graphics Indigo (R3000) with the
: insightII/Discover package along with Sculpt for the PowerMac, and not
: a whole lot of money. I would greatly appreciate any comments.


look at Protein Eng., Vol. 10, no. 1, pp. 7-21, 1997 and references


Thomas Hamelryck, thamelry at vub.ac.be
Laboratorium voor Ultrastructuur, VIB-VUB
Paardenstraat 65, B-1640 St-Genesius-Rode
"Een vogelbekdier is een dier met een bek 
  in de vorm van de poot van een eend"
                              -N. Loverix

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