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We previously described the representation of protein 3D structures inspherical coordinates (rho, phi, theta) and two of its applications: separationof the outer layer (OL) from the inner core (IC) of proteins, and assessment ofprotein surface protrusions and invaginations (Reyes, V.M., 2011& 2009). Herewe present results demonstrating the performance success of the FORTRAN 77 and90 programs used in the implementation of the two said applications, and how toimplement both applications. In particular, we show here data that demonstratethe success of our OL-IC separation procedure using a subset of the Laskowskiet al. (1996) dataset. Using a theoretical model protein in the form of ascalene ellipsoid grid of points with and without an artificially constructedprotrusion or invagination, we also show results demonstrating that protrusionsand invaginations on the protein surface maybe predicted. The nine programs wepresent here and their respective functions are: find_molec_centr.f: finds thex-, y- and z-coordinates of the protein molecular geometric centroid,cart2sphere_degrees.f90: converts PDB protein coordinates to spherical, withphi and theta in degrees, cart2sphere_radians.f90: does the same thing as thesecond program, but with phi and theta in radians, spher2cart_degrees.f90:converts the coordinates from spherical back to PDB, where input phi and thetaare in degrees, spher2cart_radians.f90: does the same thing as the fourthprogram, but with phi and theta in radians, find_rho_cutoff.f: determines therho cut-off for finding the boundary between OL and IC,phi6_theta8_binning.f90: performs the binning of phi in six- and theta ineight-degree increments, phi10_theta10_binning.f90: performs the binning of phiand theta both in ten-degree increments, and bin_rho.f90: performs the binningof rho values for plotting the frequency distribution of maximum rho values.

Implementation of the Spherical Coordinate Representation of Protein 3D Structures and its Applications Using FORTRAN 77/90 Language