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1 REFERENCES
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3 1. Wall, L.; Christiansen, T.; Schwartz, R.L. Programming Perl, 2nd edition. O'Reilly Media Inc., September 1996.
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5 2. CPAN: Comprehensive Perl archive network. [ URL: www.cpan.org ]
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6
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7 3. FSF: Free software foundation. [ URL: www.fsf.org ]
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8
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9 4. Knuth, D.E. The art of computer programming. Vol. 1-3. 2nd edition. Addison-Wesley, September 1998.
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11 5. Press, W.H.; Teukolsky, S.A.; Vetterling, W.T.; Flannery, B.P. Numerical recipies in C: the art of scientific computing. 2nd edition. Cambridge University Press, 1992.
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13 6. Orwant, J.; MacDonald, J.; Hietaniemi, J. Mastering algorithms with Perl. O'Reilly Media Inc., August 1999.
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15 7. Data for elements in the periodic table. [ URL: www.webelements.com ]
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16
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17 8. Isotope data for elements in the periodic table. [ URL: http://physics.nist.gov/PhysRefData/Compositions/index.html ]
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19 9. Main data source for amino acids. [ URL: www.expasy.ch ]
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21 10. PerlMol - Perl modules for molecular chemistry. [ URL: www.perlmol.org ]
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22
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23 11. OpenBabel: The open source chemistry toolbox. [ URL: http://openbabel.sourceforge.net/wiki/Main_Page ]
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25 12. CDK: The chemistry development kit. [ URL: http://cdk.sourceforge.net ]
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27 13. JOELIB. [ URL: http://sourceforge.net/projects/joelib/ ]
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28
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29 14. CTFile Formats. [ URL: http://accelrys.com/products/informatics/cheminformatics/ctfile-formats/no-fee.php ]
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31 15. Conway, D. Object oriented Perl. 1st edition. O'Reilly Media Inc., January 2000.
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33 16. Friedl, J.E.F. Mastering regular expressions. 3rd edition. O'Reilly Media Inc., August 2006.
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35 17. Schulz, G.E.; Schirmer, R.H. Principles of protein structure. Springer-Verlag, January 1997.
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36
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37 18. Saenger, W. Principles of nucleic acid structure. Springer-Verlag, 1983.
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39 19. Cornish-Bowden, A. Nomenclature for incompletely specified bases in nucleic acid sequence. Nucleic Acids Res. 1985, 13, 3021-3030.
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41 20. Clapham, C. A concise Oxford dictionary of mathematics. Oxford University Press, 1990.
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42
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43 21. Cook, J.L. Conversion factors. Oxford University Press, 1993.
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44
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45 22. Pauling, L. The nature of chemical bond. 3rd edition. Cornell University Press, June 1960.
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47 23. Daylight theory manual. [ URL: www.daylight.com/dayhtml/doc/theory/index.html ]
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48
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49 24. Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Am. Chem. Soc. 1988, 28, 31-36.
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51 25. Weininger, D.; Weininger, A.; Weininger, J.L. SMILES. 2. Algorithm for generation of unique SMILES notation. J. Am. Chem. Soc. 1989, 29, 97-101.
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53 26. Weininger, D. SMILES. 3. Depit. Graphical depiction of chemical structures. J. Am. Chem. Soc. 1990, 30, 237-243.
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54
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55 27. OEChem TK manual. [ URL: http://eyesopen.com/docs/toolkits/current/pdf/OEChem_TK-c++.pdf ]
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57 28. Parkin, G. Valence, oxidation number, and formal charge: Three related but fundamentally different concepts. J. Chem. Educ. 2006, 83, 791-799.
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58
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59 29. Gateiger, J.; Jochum, C. An algorithm for the perception of synthetically important rigngs. J. Chem. Inf. Comput. Sci. 1979, 19, 43-47.
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61 30. Balducci, R.; Pearlman, R.S. Efficient exact solution of the ring perception problem. J. Chem. Inf. Comput. Sci. 1994, 34, 822-831.
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63 31. Hanser, T.; Jauffret, P.; Kaufmann, G. A new algorithm for exhaustive ring perception in a molecular graph. J. Chem. Inf. Comput. Sci. 1996, 36, 1146-1152.
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64
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65 32. Cahn, R.S.; Ingold, C.; Prelog, V. Specification of molecular chirality. Angew. Chem. Internat. Edit. 1966, 5, 385-415.
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67 33. Prelog, V.; Helmchen, G. Basic principles of the CIP-system and proposals for revision. Angew. Chem. Internat. Edit. 1982, 21, 567-583.
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69 34. Mata, P.; Lobo, A.M.; Marshall, C.; Johnson, P.A. The CIP seqeunce rules: Analysis and proposal for a revision. Tetrahedron. 1993, 4, 657-668.
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70
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71 35. Nourse, J.G.; Carhart, R.E.; Smith, D.H.; Djerassi, C. Exhaustive generation of stereoisomers for structure elucidation. J. Am. Chem. Soc. 1979, 101, 1216-1223.
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72
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73 36. Nourse, J.G.; Smith, D.H.; Carhart, R.E.; Djerassi, C. Computer-assisted elucidation of molecular structue with stereochemistry. J. Am. Chem. Soc. 1980, 102, 6289-6295.
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75 37. Fused ring systems. [ URL: www.chem.qmul.ac.uk/iupac/fusedring/ ]
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77 38. A hash function for hash table lookup. [ URL: www.burtleburtle.net/bob/hash/doobs.html ]
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79 39. Ralaivola, L.; Swamidass, S.J.; Saigo, H.; Baldi, P. Graph kernals for chemical informatics. Neural Networks. 2005, 18, 1093-1110.
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80
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81 40. Willett. P.; Barnard, J.M.; Downs, G.M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
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83 41. Holliday, J.D.; Hu, C-Y.; Willett, P. Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings, Combinatorial Chemistry & High Throughput Screening. 2002, Vol. 5, No. 2, 155-166.
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85 42. Flinger, M.; Verducci, J.; Blower, P. A modification of the Jacard-Tanimoto similarity index for diverse selection of chemical compounds using binary strings. Technometrics. 2002, 44, 110-119.
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87 43. Wang, Y.; Bajorath, J. Balancing the influence of molecular complexity in fingerprint similarity searching. J. Chem. Inf. Comput. Sci. 2008, 48, 75-84.
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89 44. Flower, D.R. On the properties of bit string-based measures of chemical similarity. J. Chem. Inf. Comput. Sci. 1998, 38, 379-386.
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91 45. The Enkfil.dat and Eksfil.dat files: The keys to understanding MDL keyset technology. [ URL: http://accelrys.com/products/pdf/keys-to-keyset-technology.pdf ]
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93 46. Durant, J.L.; Leland, B.A.; Henry, D.H.; Nourse, J.G. Reoptimization of MDL Keys for Use in Drug Discovery. J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280.
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95 47. Description of public MACCS keys. [ URL: https://list.indiana.edu/sympa/arc/chminf-l/2007-11/msg00058.html ]
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96
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97 48. Morgan, H.L. The generation of a unique machine description for chemical structures - A technique developed at chemical abstracts service. J. Chem. Doc. 1965, 5, 107-112.
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98
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99 49. Penny, R.H. A connectivity code for use in describing chemical structures. J. Chem. Doc. 1965, 5, 113-117. J. Chem. Doc. 1973, 3, 153-157.
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101 50. Adamson, G.W.; Cowell, J.; Lynch, M.F.; McLure, A.H.; Town, W.G. Yapp, M. Strategic considerations in design of a screening system for substructure searches of chemical structure files.
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102
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103 51. Wipke, W.T.; Krishnan, S.; Ouchi, G.I. Hash functions for rapid storage and retrieval of chemical structures. J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280. 1978, 18, 31- .
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104
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105 52. Rogers, D.; Hahn, M. Extended-connectivity fingerprints. J. Chem. Inf. Mod. 2010, 50, 742-754.
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107 53. Faulon, J.-L.; Visco, D.P., Jr.; Pophale, R.S. The Signature Molecular Descriptor. 1. Using extended valence sequences in QSAR and QSPR studies. J. Chem. Inf. Comput. Sci. 2003, 43, 707-720.
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108
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109 54. Faulon, J.-L.; Collins, M.J.; Carr, R.D. The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences. J. Chem. Inf. Comput. Sci. 2004, 44, 427-436.
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111 55. Bender, A.; Mussa, H.Y.; Glen, R.C.; Reiling, S. Molecular similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178.
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113 56. Bender, A.; Mussa, H.Y.; Glen, R.C.; Reiling, S. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance. J. Chem. Inf. Comput. Sci. 2004, 44, 1708-1718.
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115 57. Carhart, R.E.; Smith, D.H.; Venkataraghavan, R. Atom pairs as molecular features in structure-activity studies: Definition and application. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
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116
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117 58. Nilakantan, R.; Bauman, N.; Dixon, J.S.; Venkataraghavan, R. Topological torsion: A new molecular descriptor for SAR applications. Comparison with other descriptors. J. Chem. Inf. Comput. Sci. 1987, 27, 82-85.
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119 59. Langham, J.L.; Jain, A.N. Accurate and interpretable computational modeling of chemical mutagenicity. J. Chem. Inf. Comput. Sci. 2008, 48, 1833-1839.
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121 60. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. Scaffold-hopping by topological pharmacophore search: A contribution to virtual screening. Angew. Chem. Int. Ed. 1999, 38, 2894-2896.
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123 61. Fechner, U.; Franke, L.; Renner, S.; Schneider, P. Schneider, G. Comparison of correlation vector methods for ligand-based similarity searching. J. Comput. Aided Mol. Des. 2003, 17, 687-698.
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125 62. Fechner, U.; Schneider, G. Evaluation of distance metrics for ligand-based similarity searching. ChemBioChem. 2004, 5, 538-540.
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127 63. Downs, G.M.; Willett, P.; Fisanick, W. Similarity searching and clustering of chemical-structure databases using molecular property data. J. Chem. Inf. Comput. Sci., 1994, 34, 1094-1102.
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129 64. Chen, X.; Reynolds, C.H.; Performance of similarity measures in 2D fragment-based similarity searching: Comparison of structural descriptors and similarity coefficients. J. Chem. Inf. Comput. Sci. 2002, 42, 1407-1414.
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131 65. Steffen, R.; Fechner, U.; Schneider, G. Alignment-free pharmacophore patterns: A correlation-vector approach. Pharmacophores and pharmacophore searches. 2006. Volume 32. Wiley-VCH. 49-80.
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133 66. McGregor, M.J.; Muskal, S. M. Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J. Chem. Inf. Comput. Sci. 1999, 39, 569-574.
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135 67. Floyd, R.W. Algorithm 97: Shortest path. Communications of the ACM. 1962, 5, 345.
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137 68. Horvath, D. Topological pharmacophores. Cheminformatics approaches to virtual screening. 2008. RSC Publishing. 44-75.
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139 69. Ewing, T.; Baber, C.; Feher, M. Novel 2D fingerprints in ligand-based virtual screening. J. Chem. Inf. Model. 2006, 46, 2423-2431.
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141 70. Watson, P. Naive Bayes classification using 2D pharmacophore feature triplet vectors. J. Chem. Inf. Model. 2008, 48, 166-178
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143 71. Bonachera, F.; Parent, B.; Barbosa, F.; Froloff, N.; Horvath, D. Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes. J. Chem. Inf. Model., 2006, 46, 2457-2477.
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145 72. Kearsley, S.K.; Sallamack, S.; Fluder, E.M.; Andose, J.D.; Mosley, R.T.; Sheridan, R.P. Chemical Similarity Using Physiochemical Property Descriptors.J. Chem. Inf. Comput. Sci., 1996, 36, 118-127.
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147 73. Filimonov, D.; Poroikov, V.; Borodina, Y.; Gloriozova, T. Chemical similarity assessment through multilevel neighborhoods of atoms: Definition and comparison with the other Descriptors. J. Chem. Inf. Comput. Sci., 1999, 39, 666-670.
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149 74. RDKit - Cheminformatics and Machine Learning Software. [ URL: www.rdkit.org ]
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151 75. Kier, L.B.; Hall, L.H. Electrotopological state indices for atom types: A novel combination of electronic, topological, and valence state information. J. Chem. Inf. Comput. Sci. 1995, 35, 1039-1045.
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153 76. Kier, L.B.; Hall, L.H. Molecular structure description - The electrotopological state. Academic Press, 1999.
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