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Ligand burial depth is an indicator of protein flexibility, as the extent ofreceptor conformational change required to bind a ligand in general variesdirectly with its depth of burial. In a companion paper (Reyes, V.M. 2015a), wereport on the Tangent Sphere (TS) and Cutting Plane (CP) methods --complementary methods to quantify, independent of protein size, the degree ofligand burial in a protein receptor. In this report, we present results thatdemonstrate the effectiveness of a set of FORTRAN 77 and 90 source codes usedin the implementation of the two related procedures, as well as the preciseimplementation of the procedures. Particularly, we show here that applicationof the TS and CP methods on a theoretical model protein in the form of aspherical grid of points accurately portrays the behavior of the TS and CPindices, the predictive parameters obtained from the two methods. We also showthat results of the implementation of the TS and CP methods on six proteinreceptors (Laskowski et al. 1996) are inagreement with their findings regardingcavity sizes in these proteins. The six FORTRAN programs we present here are:find_molec_centr.f, tangent_sphere.f, find_CP_coeffs.f, CPM_Neg_Side.f,CPM_Pos_Side.f and CPM_Zero_Side.f. The first program calculates the x-, y- andz-coordinates of the molecular geometric centroid of the protein (globalcentroid, GC), the center of the TS. Its radius is the distance between the GCand the local centroid (LC), the centroid of the bound ligand or a portion ofits binding site. The second program finds the number of protein atoms inside,outside and on the TS. The third determines the four coefficients A, B, C and Dof the equation of the CP, Ax + By + Cz + D = 0. The CP is tangent to the TS atGC. The fourth, fifth and sixth programs determine the number of protein atomslying on the negative side, positive side, and on the CP.

Implementation of the Tangent Sphere and Cutting Plane Methods in the  Quantitative Determination of Ligand Binding Site Burial Depths in Proteins  Using FORTRAN 77/90 Language