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Transformation of protein 3D structures from their all-atom representation(AAR) to the double-centroid reduced representation (DCRR) is a prerequisite tothe implementation of both the tetrahedral three-dimensional search motif (3DSM) method for predicting specific ligand binding sites (LBS) in proteins, andthe 3D interface search motif tetrahedral pair (3D ISMTP) method for predictingbinary protein-protein interaction (PPI) partners (Reyes, V.M., 2015a & c,2015b, 2009a, b & c). Here we describe results demonstrating the efficacy ofthe set of FORTRAN 77 and 90 source codes used in the transformation from AARto DCRR and the implementation of the 3D SM and 3D ISMTP methods. Precisely, weshow here the construction of the 3D SM for the biologically important ligands,GTP and sialic acid, from a training set composed of experimentally solvedstructures of proteins complexed with the pertinent ligand, and theirsubsequent use in the screening for potential receptor proteins of the twoligands. We also show here the construction of the 3D ISMTP for the binarycomplexes, RAC:P67PHOX and KAP:phospho-CDK2, from a training set composed ofthe experimentally solved complexes, and their subsequent use in the screeningfor potential protomers of the two complexes. The 15 FORTRAN programs used inthe AAR to DCRR transformation and the implementation of the two said methodsare: get_bbn.f, get_sdc.f, res2cm_bbn.f, res2cm_sdc.f, nrst_ngbr.f,find_Hbonds.f, find_VDWints.f, find_clusters.f90, find_trees.f90,find_edgenodes.f90, match_nodes.f, fpBS.f90, Gen_Chain_Separ.f,remove_H_atoms.f and resd_num_reduct.f. Two flowcharts - one showing how toimplement the tetrahedral 3D SM method to find LBSs in proteins, and anotherhow to implement the 3D ISMTP method to find binary PPI partners - arepresented in our two companion papers (Fig. 2, Reyes, V.M., 2015a, Fig. 1 & 2,Reyes, V.M., 2015c).

Implementation of The Double-Centroid Reduced Representation of Proteins  and its Application to the Prediction of Ligand Binding Sites and  Protein-Protein Interaction Partners Using FORTRAN 77/90 Language