

Hi, Jeremy.
 
> * Roughly how hard is it to model changes in structure or binding 
> resulting from a single point mutation? (apparantly many such typical
> mutations are from charged to uncharged residues). Is it feasible to 
> obtain meaningful results, given the state of the art? (obviously this 
> will depend on the given system, but perhaps some out there have 
> attempted this kind of problem previously.)

Our HyperChem software trivially allows single-point mutations of
proteins, and allows specific control over secondary-conformation
details.  The Sequence Editor module of the ChemPlus enhancements
package is convenient for editing or generating proteins on a more
abstract level, and then the resulting sequence can be returned to
HyperChem.
 
> * What kinds of tools are necessary or useful? (e.g. AMBER, MD, MC, 
> simulated annealing, semi-empirical calculations on local regions with 
> substrate binding, etc.) Which software packages are recommended
> (anything cheaper than Biosym?) and what level of hardware?

HyperChem will do all of the above except MC, with annealing being 
done via scripts or an external controller such as Visual Basic or 
Excel.  The suggested retail price for HyperChem is US$1995 commercial/
$995 academic.  Hardware requirements are a 386-or-better PC 
with math coprocessor, minimum 4MB RAM (it would be better to have 
considerably more RAM for macromolecule work), Windows 3.1, and the 
sorts of display, etc. that are standard with a system of that level.

Regards,
Joel
 
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Joel Polowin, Ph.D.   Manager, Scientific Support
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