need help with solvation energies...

John Kuszewski johnk at loglady.ninds.nih.gov
Mon Jan 17 14:13:08 EST 1994


Lorraine M Rellick writes:
|> Could someone point me in the direction of the latest 
|> work being done on incorporation of solvation energies
|> in peptide folding algorithms?
|> Thanks - Lori

I just gave a talk on this.  See "Surface area included in
energy refinement of proteins:  A comparative study on
atomic
solvation parameters" W. Braun et al. JMB 233, 275 (1993)
for an overview.

Scheraga's ECEPP also includes surface area calculations--the
algorithm is very fast but not always right.  See "MSEED:  A 
program for the rapid analytical determination of accessible
surface areas and their derivatives", H. Scheraga et al., J.
Computational Chem. 13, 1-11 (1992).  Scheraga seems to think
he has the folding problem solved with ECEPP, but I disagree.

Finally, a plug for some code written by Yours Truly:  an
extension to X-PLOR (a molecular dynamics / distance geometratio
popular with people who solve structures) that handles
solvation energy as well.  It's not that fast right now, but
it'll get better.  It's very flexible though.  Right now, I have
solvation numbers from K.P. Murphy and E. Freire working (can't
find the ref for their paper), and I just about have G.I. 
Makhatadze and P. Privalov's numbers (JMB 232, 639 (1993))
going too.  Write me if you're interested in this code--I have
no idea how I'll distribute it yet.

-- 
John Kuszewski
johnk at spasm.niddk.nih.gov
I'm not an idiot, but I play one on USENET.



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