Naccess V2.1.1 - Solvent accessible area calculations
calculates the atomic accessible area when a probe is rolled around the Van der Waal's
surface of a macromolecule. Such 3-dimensional co-ordinate sets (PDB files) are available from
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.
The calculation makes successive thin slices through the 3D molecular
volume to calculate the accessible surface of individual atoms, and hence is
an approximation - thinner slices improves the accuracy.
Naccess can be run with ...
- user-defined probe size
- user-defined residues (amino, nucleic and heteroatom)
- 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
- a calculation log file
- A Linux/Unix-based system
- A Fortran 77 compiler (e.g. g77 or gfortran)
is written in (fairly) standard FORTRAN 77, and runs on most Unix platforms (including most linuxes, cygwin and people have got
it working on macs). The program itself is controlled by a C-Shell script. It does not require vast
amounts of memory and is reasonably fast. You will need a Unix system and a Fortran compiler to install the
Accessiblities are widely used in the macromolecular modelling community, and
Naccess can be used to calculate both atomic and residue accessible
surfaces, for amino and nucleic acids. The output from the program can also be read in by 2 programs
available from the Biomolecular Structure and Modelling Unit at UCL:-
.. which calculates hydrogen bonds, hydrogen atom positions and can suggest
optimal conformations for Asn, Gln and His
sidechains. [Written by Ian McDonald].
.. which automatically generates schematic diagrams of
protein-ligand interactions for a given PDB file. [Written
by Andrew Wallace & Roman Laskowski].
NACCESS is (c) S. Hubbard and J. Thornton 1992-6