accessible surface area

Jeff R. Livingstone sidereal at intac.com
Tue Mar 28 02:02:28 EST 1995


In Article <1995Mar22.194113.4776 at alw.nih.gov>, johnk at spasm.niddk.nih.gov
(John Kuszewski) wrote:
>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.
>-- 

Forget Connelly's MS program. The answers for various surfaces sometimes
don't come out right. Use Tim Richmond's program instead. If anyone's
interested I'll dredge it out of the graduate student archive tapes and make
it accessible via FTP or WWW.

==========================================================================
Jeff R. Livingstone, Ph.D.                 Email:  sidereal @ intac.com
Senior Applications Scientist              Office: (800) 631-1369 ext. 493
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