|
635. SIMVOL: A Program to Calculate the Volumes, Areas, RMS
Overlap, and Percent Similarity and Identicality of Two
Molecules
by Brian T. Luke, IBM Kingston, Neighborhood Road,
Kingston, New York 12401
The program SIMVOL is written to perform each of the
following tasks:
1. Read a structure from a disk file that contains
its coordinates in Protein Data Bank (PDB) format.
2. Calculate its surface area and volume. This
includes a listing of the percent of the surface area
covered by each type of atom, as determined from the
atom's label in the input file, and for each type of
residue listed in the PDB file.
3. Read a second structure from a disk file in PDB
format.
4. Minimize the root-mean-squared (RMS) error in the
positions of a set of atoms from each structure.
5. Calculate the surface area and volume of the
second structure. This also includes a listing of
the percent of the surface area covered by each type
of atom, as determined from the atom's label in the
input file, and for each type of residue listed in
its PDB file.
6. Calculate the overall percent similarity and
percent identicality of the two structures.
7. Calculate the percent similarity and percent
identicality of each atom in each structure.
8. Calculate the percent similarity and percent
identicality for each atom name in each structure, as
determined by the atom labels in each PDB file.
9. Calculate the percent similarity and percent
identicality for each residue in each structure, as
determined by the residue names in each PDB file.
10. Generate a plot file, in addition to a file of
overlapped structures in PDB format, which can be
used to graphically display regions of similarity or
differences in the structures.
SIMVOL lets you scale the Van der Waals radius of each
atom and include a constant "probe" radius in all
calculations. A molecule's volume and surface area and
the degree of similarity of two structures are
determined using the procedure described by M. Marsili,
P. Floersheim, and A. S. Dreiding, Computers &
Chemistry, 7(4), 175-181 (1983).
Lines of Code: 1927
FORTRAN 77 (VS FORTRAN, XL FORTRAN)
| 
