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We have developed these modules in the VC++ language. For building protein surfaces(module 1) we have chosen the Connolly algorithm of presentation of the surface by points.For detection of cavities on protein surfaces (module 2) we have chosen the SurfNetalgorithm as a basis and modified it. Modifications designed by us decrease the number ofalpha and beta errors; it rejects pseudo-cavities and defines cavities with the non-conicalshape of a surface. Module 3 allows one to detect hydrophobic clusters on protein surfaces;to view charge distribution in the chosen cavities and, in this way, to predict potentialprotein binding sites. The protein atom coordinates imported from PDB-files are the inputdata for all program modules. The output data of module 1 (protein surfaces) and module 2(cavities) also are saved in the PDB format and can serve as the input data for the followingmodules. Potential binding sites of the protein (output data of module 3) are saved as a listof their amino acid residues in the txt format.( a )(b)Glu229Glu228Asp227Lys225Asp224Ser226Glu229Glu228Lys225Ser226Asp227Asp224Fig. 2. Low density lipoprotein receptor (PDB ID 1N7D) and its detected cavity with rankone. (a) All receptor domains. Repeat 5 of the ligand-binding domain is marked by blackbold line. (b) Surface of repeat 5 of the ligand-binding domain of LDLR. Detected cavitywith rank one is marked by dark color. Note: The residues numbers are given according totheir numbers in the primary sequence of LDLR imported from database UniProt (IDP01130 [6]). In 1N7D these residues correspond to residues Asp203, Lys204, Ser205,Asp206, Glu207 and Glu208.For the detection of the Apo-B,E-binding site of low density lipoprotein receptor at the firststep we imported from ProteinDataBank (PDB; http://www.rcsb.org/pdb/) the 3Dstructures of LDLR (PDB ID 1N7D), repeat 5 of LDLR (PDB ID 1AJJ) and Apo-E (PDBID 1GS9). Then using our program we built surfaces and defined in the repeat 5 of LDLRcavity with rank one which form highly charged region. This cavity is formed by residuesAsp224, Lys225, Ser226, Asp227, Glu228 and Glu229 (Figure_2).We think that the region 224-229 of LDLR form its Apo-B,E-binding site and isperspective to investigate its peptide's analogues on their ability to Apo-E and Apo-B100binding.References1. Boren, J., et al. J. Clin. Invest. 101(5), 1084-1093 (1998).2. Laurie, A.T.R., Jackson, R.M. Current Protein and Peptide Science 7, 395-406 (2006).3. Laskowski, R.A., et al. Protein Sci. 5, 2438-2452 (1996).4. Laskowski, R.A. J. Mol. Graph. 13, 323-328 (1995).5. Peters, K.P., Fauck, J., Frommel, C. J. Mol. Biol. 256, 201-213 (1996).6. http://www.uniprot.org/uniprot/P01130273