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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) |