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.
Thank you for your help,
Institute of Technical Biochemistry
University of Stuttgart Email:jpleiss at tebio1.biologie.uni-stuttgart.de
Allmandring 31 Phone:(+49)-711-685-3191
D-70569 Stuttgart, Germany Fax: (+49)-711-685-3196
W3 home page: http://www.itb.uni-stuttgart.de:8080/