accessible surface area

Victor Sivozhelezov victor at sheila.ibf.unige.it
Fri Mar 31 05:01:44 EST 1995


Jeff R. Livingstone (sidereal at intac.com) wrote:
: 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

Of course, it will be interesting to compare it to both Lee & Richards and 
Connolly results.

But what is it that makes the algorithm superior to those? Is the algorithm
description published or otherwise available?

Victor Sivozhelezov, researcher






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