accessible surface area

[John Kuszewski]

In article <3ko04o$ltd at mark.ucdavis.edu>, varma at okra.ece.ucdavis.edu (Hemant Varma) writes:
|>              I am looking for a computer alogorithm that would do
|> a good job of computing the accessible surface area in a protein.
|> I know that the method of Lee and Richards is widely used, but I 
|> was wondering if that is considered  to be a standard or are there
|> any other (better) methods out there?

There are several algorithms for calculating ASAs.  They all
produce numbers that are very close to each other.  Lee and
Richards is particularly easy to code up, so it's widely
used.  

If you want the partial derivatives of the ASA wrt the atom
coordinates, then Connelly's (sp?) work does the best job.
It looks like a bear to turn into a program, though.  I think
that Connelly is on the Internet and will sell you a program
that does ASAs and a whole lot more for a couple hundred bucks.
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John Kuszewski                     ||  |/  /|  ||      
johnk at spasm.niddk.nih.gov          ||  /  /||  ||
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