Juergen Pleiss (jpleiss at tebio1.biologie.uni-stuttgart.de) wrote:
: we are searching for a program which calculates the total hydrophobic,
: solvent accessible surface of a protein or a small molecule.
: It should read in a PDB file and output the surface area in Angstrom**2,
: which is hydrophobic _and_ solvent accessible (hydrophobicity defined by
: any of the hydrophobicity scales, solvent defined by a probe radius).
: Ideally, the program uses a user editable parameter file, which
: equivalences atom names (as given in the PDB file), VdW radius and
: hydrophobicity index, so that the user can add atoms to it.
: I would be glad if you could point me to such a program.
while you didn't specify a platform, the first one that comes to mind
is hyperchem for the pc. we use it here to do just that, to calculate
water accessable surface areas with varying probe sizes. hyperchem can
read in a pdb file and you can use it to select hydrophobic resiues and
from there calculate the ASA.
as for other platforms, there exist a plethora of such programs on UNIX
boxes. as far as macintosh and powermacs go, i am at a loss to provide
you with information as to what programs will fill your needs.
jose at lpoly.bioc.cwru.edu