Hemant Varma (varma at okra.ece.ucdavis.edu) wrote:
: Hello Folks,
: I was wondering if any body knew of some computer
: algorithms for computing accessible surface areas in proteins.
: I know that the method of Lee and Richards is very much in use,
: but is that the only standard method of doing so? Or are there
: any more better methods out there?
Naccess v2.0 - Atomic solvent accessible areas
Written by Simon Hubbard
Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB file.
The program uses the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method, whereby a probe of
given radius is rolled around the surface of the molecule, and the path traced out by its centre is the
accessible surface. Typically, the probe has the same radius as water (1.4 Angstroms) and hence the
surface described is often referred to as the solvent accessible surface.
Naccess can be run with ...
user-defined probe size
user-defined atomic radii
user-defined "standard state" residue accessibilities
with/without hetatoms, hydrogens, waters
a file of atomic accessible areas
a file of summed absolute and relative residue accessible areas
is written in (fairly) standard FORTRAN 77, and runs on most Unix platforms. A VAX/VMS version
will be available if there is any demand. The program itself is controlled by a C-Shell script (Unix
version). It does not require vast amounts of memory and is reasonably fast (about 8 real time seconds on
an old IRIS Indigo workstation for the protein crambin 1crn).
The ouput from the program can be read in by:-
HBPLUS - which calculates hydrogen bonds, hydrogen positions and can suggest optimal
conformations for Asn, Gln and His sidechains. [Written by Ian McDonald].
LIGPLOT - which automatically generates schematic diagrams of protein-ligand
interactions for a given PDB file. [Written by Andrew Wallace & Roman Laskowski].
How to get it
You can get a compressed tar file containing everything you need by clicking here . You can also have a
look at the README file to get more of an idea about the program before downloading it.
NACCESS is (c) S. Hubbard and J. Thornton 1992-4