jpleiss at tebio1.biologie.uni-stuttgart.de (Juergen Pleiss) writes:
> 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.
It is possible to do this with Grasp. You may need a bit work to
get started, but as you are able to control Grasp via scripts,
much of the hard work can be made automatic. We have used this
to look at the amount of surface area of hydrophobic nature,
or with electrostatic potential within a certain range, or involved
in hydrogen bonding etc, for various molecules and complexes.
---
Finn Drablos finn.drablos at unimed.sintef.no
SINTEF UNIMED Biotech http://www.mr.sintef.no/
N-7034 TRONDHEIM phone +47 73 59 02 18
NORWAY fax +47 73 59 02 20
