? HELP : "Acessibilities" /standart /please

felix vajdos felix at alta.med.utah.edu
Sat Apr 19 16:17:30 EST 1997

Ivan Yu. Torshin wrote:
> Hello,
> I'm very sorry to send this for the third time,
> may be it is a fuulishsh kueshn,
>                        BUT
> Would anyone consult me,
> if all atom temperature factors
> are given
> (as they are in PDB file)
> are there any other
> (except simple average)
> reasonable ways to calculate factor for residue ?

As far as I know, probably the most reasonable way of calculating a "per
residue" temperature factor is to simply average the temp factors for
the side chain and main chain atoms seperatly (i.e.  two temp. factors
for each residue, the average main chain B-factors and the average side
chain B-factors).  I believe the program 4d_moleman from Gerard Klewygt
will do this type of operation after reading in a standard pdb file.

> Also, where can I get table of standard accessibilities for
> amino acid residues ?

I'm not sure what you mean by "standard accessibilities".  If you want
to know how solvent accessible each residue is, there are many
variations on the Lee and Richards algorithm for calculating surface
accesibility (we use one called NACCESS).  If you want to know how your
accessibilities compare with other structures, I don't know if anyone
has done such a survey.  There are algorithms for determining the
probability of finding residue X in microenvironment Y (i.e. Bowie's
3D-1D program)

Good Luck,
Felix F. Vajdos
University of Utah
Department of Biochemistry

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