Protein modelling software for PowerMacs (was: (none))

Harry Mangalam mangalam at uci.edu
Tue Apr 9 11:11:57 EST 1996


> In article <4kbe18$kdj at winx03.informatik.uni-wuerzburg.de>,
krasel at wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) writes:
> > You might have seen on this newsgroup an announcement for the program
> > "FoldIt Light" which should do what you want (I have never tried it). 
> > However, do not expect any program to get a sequence as input and
> > spew out a structure. The protein folding problem isn't yet solved.


To which (Richard P. Grant) replied:


> You are 100% correct Cornelius.  I would it were that simple to determine 
> structure!  There are a number of ways of predicting secondary structure, if 
> you have good homology with another proteins you can do this to about 80% 
> accuracy with a program whose name escapes me, but I can look it up for you.
> It's better rated than the stuff within GCG, but maybe that dooes not say 
> much...
> 
> PredictProtein at embl-heidelberg.de is possibly what I'm thinkin - Sanders and 
> Rost did the algorithms.  Please correct me if I'm wrong.

And Harry chipped in with his 2 bits...

There are a number of secondary structure prediction sites available on
the web (BMERC, phd, SSPROT, Deleage's SOPM email service).  Try my page
that describes my first go thru them:

http://hornet.mmg.uci.edu/~hjm/projects/biocomp/structure.html

(altho the IP# and machine name will change shortly, email if the URL
doesn't work)

As well, anyone interested in protein folding with a PowerMac or SGI in
hand should check out Mark Surles' Sculpt from Interactive Simulations:

htttp://www.intsim.com

which is one of the more astonishing pieces of software that I've ever
dealt with (yeah, yeah, yeah, heard that before..).  Near real-time
minimization of surprisingly large molecules, as well as nice interface,
easy to learn and a very good educational tool (see all those bewildering
formulae spring to life in fast 3D).  Handles Van der Waals and
electrostatics, freeze/thaw different parts, complete interactivity or set
reps to a high # to relax the structure and have a few sips of coffee. 
I'm not sure about the final accuracy relative to approaches avaiable via
BIOSYM/MSI's DIscover, but they appear to be pretty close and the
validation tools available to me (ProsaII, Profiles 3D, etc) seem not to
mind.

Mark has just ported what was an SGI-only SW to the PMac and found (to MY
surprise) that a 100MHz 601 runs about 3/4 the speed of an 150MHz R4400 on
the pure computational code; I'd expect parity or better with a
evenly-clocked PPC604  Much slower and grungier graphics (but then that
extra  $25,000 to SGI has to go for something).  Nevertheless, it is WELL
worth looking at.

Disclaimer:  I've known Mark Surles professionally for several years and
have been a sporadic beta tester for both SGI and PMac versions, but have
no financial interest in his company.  But he's a terrific scientist,
programmer and interface designer.

Cheers
Harry
-- 
Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine,
      Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598
            http://hornet.mmg.uci.edu/~hjm/hjm.html
  Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW 




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