Graph applications in chemoinformatics and structural bioinformatics

Bioinformatics: Concepts, Methodologies, Tools, and Applications

Volumn 2, Issue , 2013, Pages 1126-1157

  Gardiner, Eleanor Joyce ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; MOLECULAR GRAPHICS;

3-D SPACE; CHEMICAL GRAPH THEORY; CHEMOINFORMATICS; LABELED GRAPHS; MOLECULAR GRAPHS; STRUCTURAL BIOINFORMATICS; STRUCTURAL THEORIES; THREE DIMENSIONS;

GRAPH THEORY;

EID: 84922250861     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4018/978-1-4666-3604-0.ch058     Document Type: Chapter

References (137)

1. Allen, F. H. (2002). The Cambridge structural database: A quarter of a million crystal structures and rising. Acta Crystallographica. Section B, Structural Science, 58, 380-388. doi:10.1107/ S0108768102003890
2. Artymiuk, P. J., Bath, P. A., Grindley, H. M., Pepperrell, C. A., Poirrette, A. R., & Rice, D. W. (1992). Similarity searching in databases of 3-dimensional molecules and macromolecules. Journal of Chemical Information and Computer Sciences, 32(6), 617-630. doi:10.1021/ ci00010a007
3. Artymiuk, P. J., Grindley, H. M., Kumar, K., Rice, D. W., & Willett, P. (1993). 3-dimensional structural resemblance between the ribonuclease-h and connection domains of hiv reverse-transcriptase and the atpase fold revealed using graph-theoretical techniques. FEBS Letters, 324(1), 15-21. doi:10.1016/0014-5793(93)81523-3
4. Artymiuk, P. J., Grindley, H. M., Poirrette, A. R., Rice, D. W., Ujah, E. C., & Willett, P. (1994). Identification of beta-sheet motifs, of psi-loops, and of patterns of amino-acid-residues in 3-dimensional protein structures using a subgraph-isomorphism algorithm. Journal of Chemical Information and Computer Sciences, 34(1), 54-62. doi:10.1021/ ci00017a007
5. Artymiuk, P. J., Poirrette, A. R., Grindley, H. M., Rice, D. W., & Willett, P. (1994). A graph-theoretic approach to the identification of 3-dimensional patterns of amino-acid side-chains in protein structures. Journal of Molecular Biology, 243(2), 327-344. doi:10.1006/jmbi.1994.1657
6. Artymiuk, P. J., Poirrette, A. R., Rice, D. W., & Willett, P. (1997). A polymerase 1 palm in adenylyl cyclase? Nature, 388, 33-34. doi:10.1038/40310
7. Balaban, A. T. (1982). Highly discriminating distance-based topological index. Chemical Physics Letters, 89(5), 399-404. doi:10.1016/0009-2614(82)80009-2
8. Balaban, A. T., & Harary, F. (1971). Characteristic polynomial does not uniquely determine topology of a molecule. Journal of Chemical Documentation, 11(4), 258. doi:10.1021/c160043a020
9. Barker, E. J., Buttar, D., Cosgrove, D. A., Gardiner, E. J., Kitts, P., & Willett, P. (2006). Scaffold hopping using clique detection applied to reduced graphs. Journal of Chemical Information and Modeling, 46(2), 503-511. doi:10.1021/ci050347r
10. Barker, E. J., Gardiner, E. J., Gillet, V. J., Kitts, P., & Morris, J. (2003). Further development of reduced graphs for identifying bioactive compounds. Journal of Chemical Information and Computer Sciences, 43(2), 346-356. doi:10.1021/ci0255937
11. Barnard, J. M. (1993). Substructure searching methods-old and new. Journal of Chemical Information and Computer Sciences, 33(4), 532-538. doi:10.1021/ci00014a001
12. Ben-Dor, A., Shamir, R., & Yakhini, Z. (1999). Clustering gene expression patterns. Journal of Computational Biology, 6(3-4), 281-297. doi:10.1089/106652799318274
13. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., & Rodgers, J. R. (1977). Protein data bank-computer-based archival file for macromolecular structures. Journal of Molecular Biology, 112(3), 535-542. doi:10.1016/ S0022-2836(77)80200-3
14. Birchall, K., Gillet, V. J., Harper, G., & Pickett, S. D. (2008a). Evolving interpretable structure-Activity relationship models. 2. Using multiobjective optimization to derive multiple models. Journal of Chemical Information and Modeling, 48(8), 1558-1570. doi:10.1021/ci800051h
15. Birchall, K., Gillet, V. J., Harper, G., & Pickett, S. D. (2008b). Evolving interpretable structure-Activity relationships. 1. Reduced graph queries. Journal of Chemical Information and Modeling, 48(8), 1543-1557. doi:10.1021/ci8000502
16. Brint, A. T., & Willett, P. (1987a). Algorithms for the identification of 3-dimensional maximal common substructures. Journal of Chemical Information and Computer Sciences, 27(4), 152-158. doi:10.1021/ci00056a002
17. Brint, A. T., & Willett, P. (1987b). Pharmacophoric pattern-matching in files of 3d chemical structures-Comparison of geometric searching algorithms. Journal of Molecular Graphics, 5(1), 49-56. doi:10.1016/0263-7855(87)80045-0
18. Bron, C., & Kerbosch, J. (1973). Finding all cliques of an undirected graph. Communications of the ACM, 16(9), 575-577. doi:10.1145/362342.362367
19. Brown, F. K. (1998). Chemoinformatics: What is it and how does it impact drug discovery? Annual Reports in Medicinal Chemistry, 33, 375-384. doi:10.1016/S0065-7743(08)61100-8
20. Brown, N. (2009). Chemoinformatics-An introduction for computer scientists. ACM Computing Surveys, 41(2), 38. doi:10.1145/1459352.1459353
21. Bruno, I. J., Kemp, N. M., Artymiuk, P. J., & Willett, P. (1997). Representing and searching of carbohydrate structures using graph-theoretic techniques. Carbohydrate Research, 304, 61-67. doi:10.1016/S0008-6215(97)00196-1
22. Carraghan, R., & Pardalos, P. M. (1990). An exact algorithm for the maximum clique problem. Operations Research Letters, 9(6), 375-382. doi:10.1016/0167-6377(90)90057-C
23. Cheeseright, T., Mackey, M., Rose, S., & Vinter, A. (2006). Molecular field extrema as descriptors of biological activity: Definition and validation. Journal of Chemical Information and Modeling, 46(2), 665-676. doi:10.1021/ci050357s
24. Crandell, C. W., & Smith, D. H. (1983). Applications of artificial intelligence for chemical interference. 44. Computer-assisted examination of compounds for common 3-dimensional substructures. Journal of Chemical Information and Computer Sciences, 23(4), 186-197. doi:10.1021/ ci00040a009
25. De Jong, H. (2002). Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology, 9(1), 67-103. doi:10.1089/10665270252833208
26. Decker, R., Lenz, H. J., & Borgelt, C. (2007). Canonical forms for frequent graph mining. In Advances in Data Analysis (pp. 337-349). Berlin, Heidelberg: Springer. doi:10.1007/978-3-540-70981-7
27. DiMasi, J. A., Hansen, R. W., & Grabowski, H. G. (2003). The price of innovation: New estimates of drug development costs. Journal of Health Economics, 22(2), 151-185. doi:10.1016/S0167-6296(02)00126-1
28. Doubet, S., Bock, K., Smith, D. H., Darvill, A., & Albersheim, P. (1989). The complex carbohydrate structure database. Trends in Biochemical Sciences, 14, 475-477. doi:10.1016/0968-0004(89)90175-8
29. Ebe, T., Sanderson, K. A., & Wilson, P. S. (1991). The chemical abstracts service generic chemical (Markush) structure storage and retrieval capability. 2. The MARPAT file. Journal of Chemical Information and Computer Sciences, 31(1), 31-36. doi:10.1021/ci00001a004
30. Ewing, T. J. A., & Kuntz, I. D. (1997). Critical evaluation of search algorithms for automated molecular docking and database screening. Journal of Computational Chemistry, 18(9), 1175-1189. doi:10.1002/ (SICI)1096-987X(19970715)18:9<1175::AIDJCC6> 3.0.CO;2-O
31. Feng, J., Sanil, A., & Young, S. S. (2006). PharmID:Pharmacophore identification using Gibbs sampling. Journal of Chemical Information and Modeling, 46(3), 1352-1359. doi:10.1021/ ci050427v
32. Figueras, J. (1972). Substructure search by set reduction. Journal of Chemical Documentation, 12(4), 237-244. doi:10.1021/c160047a010
33. Figueras, J. (1996). Ring perception using breadthfirst search. Journal of Chemical Information and Computer Sciences, 36(5), 986-991. doi:10.1021/ ci960013p
34. Gardiner, E. J., Artymiuk, P. J., & Willett, P. (1997). Clique-detection algorithms for matching 3-dimensional molecular structures. Journal of Molecular Graphics & Modelling, 15(4), 245-253. doi:10.1016/S1093-3263(97)00089-2
35. Gardiner, E. J., Cosgrove, D. A., Taylor, R., & Gillet, V. J. (2009). Multiobjective optimization of Pharmacophore hypotheses: Bias toward low-energy conformations. Journal of Chemical Information and Modeling, 49(12), 2761-2773. doi:10.1021/ci9002816
36. Gardiner, E. J., Gillet, V. J., Willett, P., & Cosgrove, D. A. (2007). Representing clusters using a maximum common edge substructure algorithm applied to reduced graphs and molecular graphs. Journal of Chemical Information and Modeling, 47(2), 354-366. doi:10.1021/ci600444g
37. Gardiner, E. J., Willett, P., & Artymiuk, P. J. (2000). Graph-theoretic techniques for macromolecular docking. Journal of Chemical Information and Computer Sciences, 40(2), 273-279. doi:10.1021/ ci990262o
38. Gasteiger, J. (2006). The central role of chemoinformatics. Chemometrics and Intelligent Laboratory Systems, 82(1-2), 200-209. doi:10.1016/j. chemolab.2005.06.022
39. Gillet, V. J., Downs, G. M., Holliday, J. D., Lynch, M. F., & Dethlefsen, W. (1991). Computer-storage and retrieval of generic chemical structures in patents. 13. Reduced graph generation. Journal of Chemical Information and Computer Sciences, 31(2), 260-270. doi:10.1021/ci00002a011
40. Gillet, V. J., Downs, G. M., Ling, A., Lynch, M. F., Venkataram, P., & Wood, J. V. (1987). Computerstorage and retrieval of generic chemical structures in patents. 8. Reduced chemical graphs and their applications in generic chemical-structure retrieval. Journal of Chemical Information and Computer Sciences, 27(3), 126-137. doi:10.1021/ ci00055a007
41. Gillet, V. J., Willett, P., & Bradshaw, J. (2003). Similarity searching using reduced graphs. Journal of Chemical Information and Computer Sciences, 43(2), 338-345. doi:10.1021/ci025592e
42. Gorse, A.-D. (2006). Diversity in medicinal chemistry space. Current Topics in Medicinal Chemistry, 6, 3-18. doi:10.2174/156802606775193310
43. Grindley, H. M., Artymiuk, P. J., Rice, D. W., & Willett, P. (1993). Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. Journal of Molecular Biology, 229(3), 707-721. doi:10.1006/jmbi.1993.1074
44. Gu, J., & Bourne, P. E. (2009). Structural bioinformatics (2nd ed.). NJ, USA: Wiley-Blackwell.
45. Hagadone, T. R. (1992). Molecular substructure similarity searching-Efficient retrieval in 2-dimensional structure databases. Journal of Chemical Information and Computer Sciences, 32(5), 515-521. doi:10.1021/ci00009a019
46. Harper, G., Bravi, G. S., Pickett, S. D., Hussain, J., & Green, D. V. S. (2004). The reduced graph descriptor in virtual screening and data-driven clustering of high-throughput screening data. Journal of Chemical Information and Computer Sciences, 44(6), 2145-2156. doi:10.1021/ ci049860f
47. Hart, T. N., & Read, R. J. (1992). A multiplestart Monte-Carlo docking method. Proteins-Structure Function and Genetics, 13(3), 206-222. doi:10.1002/prot.340130304
48. Hawkins, P. C. D., Skillman, A. G., Warren, G. L., Ellingson, B. A., & Stahl, M. T. (2010). Conformer generation with OMEGA: Algorithm and validation using high quality structures from the protein databank and Cambridge structural database. Journal of Chemical Information and Modeling, 50(4), 572-584. doi:10.1021/ci100031x
49. Holm, L., & Sander, C. (1993). Protein-structure comparison by alignment of distance matrices. Journal of Molecular Biology, 233(1), 123-138. doi:10.1006/jmbi.1993.1489
50. Holm, L., & Sander, C. (1995). DALI-A network tool for protein-structure comparison. Trends in Biochemical Sciences, 20(11), 478-480. doi:10.1016/S0968-0004(00)89105-7
51. Holm, L., & Sander, C. (1998). Touring protein fold space with Dali/FSSP. Nucleic Acids Research, 26(1), 316-319. doi:10.1093/nar/26.1.316
52. Hwang, K. Y., Chung, J. H., Kim, S. H., Han, Y. S., & Cho, Y. J. (1999). Structure-based identification of a novel NTPase from Methanococcus Jannaschii. Nature Structural Biology, 6, 691-696. doi:10.1038/10745
53. Jarvis, R. A., & Patrick, E. A. (1973). Clustering using a similarity measure based on shared near neighbors. IEEE Transactions on Computers, C-22(11), 1025-1034. doi:10.1109/TC. 1973.223640
54. Johnson, D. S., & Trick, M. A. (1996). Cliques, Colorings and Satifiability: 2nd DIMACS Implementation Challenge. Bellcore and the American Mathematical Society.
55. Johnson, M. (1985). Relating metrics, lines and variables defined on graphs to problems in medicinal chemistry. In Alavi, Y., Chartrand, G., Lesniak, L., Lick, D., & Wall, C. (Eds.), Graph theory and its applications to algorithms and computer science (pp. 457-470). New York: Wiley.
56. Johnson, M. A., & Maggiora, G. M. (1990). Concepts and applications of molecular similarity. New York: Wiley Inter-Science.
57. Jonsdottir, S. O., Jorgensen, F. S., & Brunak, S. (2005). Prediction methods and databases within chemoinformatics: Emphasis on drugs and drug candidates. Bioinformatics (Oxford, England), 21(10), 2145-2160. doi:10.1093/bioinformatics/ bti314
58. Kabsch, W. (1976). Solution for best rotation to relate 2 sets of vectors. Acta Crystallographica Section A, 32(SEP1), 922-923.
59. Kasinos, N., Lilley, G. A., Subbarao, N., & Haneef, I. (1992). A robust and efficient automated docking algorithm for molecular recognition. Protein Engineering, 5(1), 69-75. doi:10.1093/ protein/5.1.69
60. Kier, L. B., & Hall, L. H. (1986). Molecular connectivity in structure-activity analysis. Chichester, UK: John Wiley and Sons.
61. Kinoshita, K., & Nakamura, H. (2003). Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Science, 12(8), 1589-1595. doi:10.1110/ps.0368703
62. Krissinel, E., & Henrick, K. (2004). Secondarystructure matching (SSM), a new tool for fast protein structure alignment in 3 dimensions. Acta Crystallographica. Section D, Biological Crystallography, 60, 2256-2268. doi:10.1107/ S0907444904026460
63. Kuhl, F. S., Crippen, G. M., & Friesen, D. K. (1984). A combinatorial algorithm for calculating ligand-binding. Journal of Computational Chemistry, 5(1), 24-34. doi:10.1002/jcc.540050105
64. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., & Ferrin, T. E. (1982). A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology, 161(2), 269-288. doi:10.1016/0022-2836(82)90153-X
65. Kuramochi, M., & Karypis, G. (2007). Discovering frequent geometric subgraphs. Information Systems, 32(8), 1101-1120. doi:10.1016/j. is.2005.05.005
66. Lander, E. S., Linton, L., Birren, B., Nusbaum, C., Zody, M., & Baldwin, J. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860-921. doi:10.1038/35057062
67. Leach, A. R., & Gillet, V. J. (2007). An introduction to chemoinformatics (2nd ed.). Dordrecht, Netherlands:Springer. doi:10.1007/978-1-4020-6291-9
68. Leach, A. R., Gillet, V. J., Lewis, R. A., & Taylor, R. (2010). 3-dimensional Pharmacophore methods in drug discovery. Journal of Medicinal Chemistry, 53(2), 539-558. doi:10.1021/jm900817u
69. Luscombe, N. M., Greenbaum, D., & Gerstein, M. (2001). What is bioinformatics? A proposed definition and overview of the field. Methods of Information in Medicine, 40(4), 346-358.
70. Lynch, M. F., & Holliday, J. D. (1996). The Sheffield generic structures project-A retrospective review. Journal of Chemical Information and Computer Sciences, 36(5), 930-936. doi:10.1021/ ci950173l
71. Martin, Y. C., Bures, M. G., Danaher, E. A., Delazzer, J., Lico, I., & Pavlik, P. A. (1993). A fast new approach to Pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists. Journal of Computer-Aided Molecular Design, 7(1), 83-102. doi:10.1007/BF00141577
72. Miller, M. D., Kearsley, S. K., Underwood, D. J., & Sheridan, R. P. (1994). FLOG-A system to select quasi-flexible ligands complementary to a receptor of known 3-dimensional structure. Journal of Computer-Aided Molecular Design, 8(2), 153-174. doi:10.1007/BF00119865
73. Mitchell, E. M., Artymiuk, P. J., Rice, D. W., & Willett, P. (1990). Use of techniques derived from graph theory to compare secondary structure motifs in proteins. Journal of Molecular Biology, 212, 151-166. doi:10.1016/0022-2836(90)90312-A
74. Molconn-Z. Retrieved December 15, 2010, from http:////www.edusoft-lc.com/molconn
75. Morgan, H. L. (1965). Generation of a unique machine description for chemical structures-A technique developed at Chemical Abstracts Service. Journal of Chemical Documentation, 5(2), 107. doi:10.1021/c160017a018
76. Pardalos, P. M., & Rebennack, S. (2010). Computational Challenges with Cliques, Quasi-cliques and Clique Partitions in Graphs. In Festa, P. (Ed.), Experimental Algorithms, Proceedings (Vol. 6049, pp. 13-22). Berlin, Germany: Springer-Verlag Berlin. doi:10.1007/978-3-642-13193-6_2
77. Podolyan, Y., & Karypis, G. (2009). Common Pharmacophore identification using frequent clique detection algorithm. Journal of Chemical Information and Modeling, 49(1), 13-21. doi:10.1021/ci8002478
78. Randic, M., & Wilkins, C. L. (1979). Graphbased fragment searches in polycyclic structures. Journal of Chemical Information and Computer Sciences, 19(1), 23-31. doi:10.1021/ci60017a008
79. Rarey, M., & Dixon, J. S. (1998). Feature trees: A new molecular similarity measure based on tree matching. Journal of Computer-Aided Molecular Design, 12(5), 471-490. doi:10.1023/A:1008068904628
80. Ray, L. C., & Kirsch, R. A. (1957). Finding chemical records by digital computers. Science, 126(3278), 814-819. doi:10.1126/science. 126.3278.814
81. Raymond, J. W., Blankley, C. J., & Willett, P. (2003). Comparison of chemical clustering methods using graph-and fingerprint-based similarity measures. Journal of Molecular Graphics & Modelling, 21(5), 421-433. doi:10.1016/S1093-3263(02)00188-2
82. Raymond, J. W., Gardiner, E. J., & Willett, P. (2002a). Heuristics for similarity searching of chemical graphs using a maximum common edge subgraph algorithm. Journal of Chemical Information and Computer Sciences, 42(2), 305-316. doi:10.1021/ci010381f
83. Raymond, J. W., Gardiner, E. J., & Willett, P. (2002b). RASCAL: Calculation of graph similarity using maximum common edge subgraphs. The Computer Journal, 45(6), 631-644. doi:10.1093/ comjnl/45.6.631
84. Raymond, J. W., & Willett, P. (2002a). Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases. Journal of Computer-Aided Molecular Design, 16(1), 59-71. doi:10.1023/A:1016387816342
85. Raymond, J. W., & Willett, P. (2002b). Maximum common subgraph isomorphism algorithms for the matching of chemical structures. Journal of Computer-Aided Molecular Design, 16(7), 521-533. doi:10.1023/A:1021271615909
86. Read, R. C., & Corneil, D. G. (1977). The graph isomorphism disease. Journal of Graph Theory, 1, 339-363. doi:10.1002/jgt.3190010410
87. Rhodes, N., Willett, P., Calvet, A., Dunbar, J. B., & Humblet, C. (2003). CLIP: Similarity searching of 3D databases using clique detection. Journal of Chemical Information and Computer Sciences, 43(2), 443-448. doi:10.1021/ci025605o
88. Rucker, C., Rucker, G., & Meringer, M. (2002). Exploring the limits of graph invariant-and spectrum-based discrimination of (sub)structures. Journal of Chemical Information and Computer Sciences, 42(3), 640-650. doi:10.1021/ci010121y
89. Rusinko, A., Skell, J. M., Balducci, R., & Pearlman, R. S. (1986). Concord-Rapid generation of high-quality approximate 3-dimensional molecular coordinates. [-COMP.]. Abstracts of Papers of the American Chemical Society, 192, 12.
90. Russo, E. (2002). Chemistry plans a structural overhaul. Nature, 419(6903), 4-7. doi:10.1038/ nj6903-04a
91. Southan, C., Varkonyi, P., & Muresan, S. (2007). Complementarity between public and commercial databases: New opportunities in medicinal chemistry informatics. Current Topics in Medicinal Chemistry, 7(15), 1502-1508. doi:10.2174/156802607782194761
92. Spriggs, R. V., Artymiuk, P. J., & Willett, P. (2003). Searching for patterns of amino acids in 3D protein structures. Journal of Chemical Information and Computer Sciences, 43(2), 412-421. doi:10.1021/ci0255984
93. Stahl, M., & Mauser, H. (2005). Database clustering with a combination of fingerprint and maximum common substructure methods. Journal of Chemical Information and Modeling, 45(3), 542-548. doi:10.1021/ci050011h
94. Stahl, M., Mauser, H., Tsui, M., & Taylor, N. R. (2005). A robust clustering method for chemical structures. Journal of Medicinal Chemistry, 48(13), 4358-4366. doi:10.1021/jm040213p
95. Stiefl, N., Watson, T. A., Baumann, K., & Zaliani, A. (2006). ErG: 2D Pharmacophore descriptions for scaffold hopping. Journal of Chemical Information and Modeling, 46(1), 208-220. doi:10.1021/ci050457y
96. Sussenguth, E. H. (1965). A graph-theoretic algorithm for matching chemical structures. Journal of Chemical Documentation, 5(1), 36. doi:10.1021/ c160016a007
97. Takahashi, Y., Sukekawa, M., & Sasaki, S. (1992). Automatic identification of molecular similarity using reduced-graph representation of chemicalstructure. Journal of Chemical Information and Computer Sciences, 32(6), 639-643. doi:10.1021/ ci00010a009
98. Ullmann, J. R. (1976). Algorithm for subgraph isomorphism. Journal of the ACM, 23(1), 31-42. doi:10.1145/321921.321925
99. Venter, J. C., Adams, M., Myers, E., Li, P., Mural, R., & Sutton, G. (2001). The sequence of the human genome. Science, 291, 1304-1351. doi:10.1126/ science.1058040
100. Villar, H. O., & Hansen, M. R. (2009). Mining and visualizing the chemical content of large databases. Current Opinion in Drug Discovery & Development, 12(3), 367-375.
101. Vonscholley, A. (1984). A relaxation algorithm for generic chemical-structure screening. Journal of Chemical Information and Computer Sciences, 24(4), 235-241. doi:10.1021/ci00044a009
102. Ward, J. H. (1963). Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association, 58(301), 236. doi:10.2307/2282967
103. Weininger, D. (1988). SMILES, a chemical language and information-system. 1. Introduction to methodology and encoding. Journal of Chemical Information and Computer Sciences, 28(1), 31-36. doi:10.1021/ci00057a005
104. Whitney, H. (1932). Congruent graphs and the connectivity of graphs. American Journal of Mathematics, 54, 150-168. doi:10.2307/2371086
105. Wiener, H. (1947). Structural determination of paraffin boiling points. Journal of the American Chemical Society, 69(1), 17-20. doi:10.1021/ ja01193a005
106. Willett, P. (2005). Searching techniques for databases of 2-and 3-dimensional chemical structures. Journal of Medicinal Chemistry, 48(13), 4183-4199. doi:10.1021/jm0582165
107. Willett, P. (2006). Similarity-based virtual screening using 2D fingerprints. Drug Discovery Today, 11(23-24), 1046-1053. doi:10.1016/j. drudis.2006.10.005
108. Willett, P., Barnard, J. M., & Downs, G. M. (1998). Chemical similarity searching. Journal of Chemical Information and Computer Sciences, 38(6), 983-996. doi:10.1021/ci9800211
109. Yan, X. F., Yu, P. S., & Han, J. (2004). Graph indexing: A frequent structure-based approach. Paper presented at the SIGMOD'04 (International Conference on Management of Data), Paris.
110. Yan, X. F., Zhu, F. D., Yu, P. S., & Han, J. W. (2006). Feature-based similarity search in graph structures. ACM Transactions on Database Systems, 31(4), 1418-1453. doi:10.1145/1189769.1189777
111. Zarembinski, T. I., Hung, L. W., Mueller-Dieckmann, H. J., Kim, K. K., Yokota, H., & Kim, R.... Kim, S. H. (1998). Structure-based assignment of the biochemical function of a hypothetical protein:A test case of structural genomics. In Proceedings of the National Academy of Sciences of the United States of America, 95, 15189-15193.
112. Artymiuk, P. J., Spriggs, R. V., & Willett, P. (2005). Graph theoretic methods for the analysis of structural relationships in biological macromolecules. Journal of the American Society for Information Science and Technology, 56(5), 518-528. doi:10.1002/asi.20140
113. Bajorath, J. (2004). Chemoinformatics: Concepts, methods and tools for drug discovery. Totowa, N.J.: Humana Press.
114. Balaban, A. T. (1995). Chemical graphs-looking back and glimpsing ahead. Journal of Chemical Information and Computer Sciences, 35, 339-350. doi:10.1021/ci00025a001
115. Barnard, J. M. (1993). Substructure searching methods-old and new. Journal of Chemical Information and Computer Sciences, 33(4), 532-538. doi:10.1021/ci00014a001
116. Brown, N. (2009). Chemoinformatics-An introduction for computer scientists. ACM Computing Surveys, 41(2), 38. doi:10.1145/1459352.1459353
117. Butenko, S., & Wilhelm, W. E. (2006). Cliquedetection models in computational biochemistry and genomics. European Journal of Operational Research, 173(1), 1-17. doi:10.1016/j. ejor.2005.05.026
118. Faulon, J.-L., & Bender, A. (2010). Handbook of chemoinformatics algorithms. Routledge.
119. Grindrod, P., & Kibble, M. (2004). Review of uses of network and graph theory concepts within proteomics. Expert Review of Proteomics, 1(2), 229-238. doi:10.1586/14789450.1.2.229
120. Gu, J., & Bourne, P. E. (2009). Structural bioinformatics (2nd ed.). Wiley-Blackwell.
121. Halperin, I., Ma, B. Y., Wolfson, H., & Nussinov, R. (2002). Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins-Structure Function and Genetics, 47(4), 409-443. doi:10.1002/prot.10115
122. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K. F., Ueda, N., & Hamajima, M. (2006). KEGG as a glycome informatics resource. Glycobiology, 16(5), 63R-70R. doi:10.1093/ glycob/cwj010
123. Jones, S., & Thornton, J. M. (2004). Searching for functional sites in protein structures. Current Opinion in Chemical Biology, 8(1), 3-7. doi:10.1016/j.cbpa.2003.11.001
124. King, R. B., & Rouvray, D. H. (1987). Graph theory and topology in chemistry. Oxford: Elsevier.
125. Koehle, P. (2006). Protein structure classification. In Lipkowitz, K. B., Cundari, T. R., & Gillet, V. J. (Eds.), Reviews in computational chemistry. Hoboken, New Jersey: Wiley. doi:10.1002/0471780367. ch1
126. Leach, A. R., & Gillet, V. J. (2007). An introduction to chemoinformatics (2nd ed.). Dordrecht:Springer. doi:10.1007/978-1-4020-6291-9
127. Leach, A. R., Gillet, V. J., Lewis, R. A., & Taylor, R. (2010). Three-dimensional pharmacophore methods in drug discovery. Journal of Medicinal Chemistry, 53(2), 539-558. doi:10.1021/ jm900817u
128. Lozano, M. A., & Escolano, F. (2006). Protein classification by matching and clustering surface graphs. Pattern Recognition, 39(4), 539-551. doi:10.1016/j.patcog.2005.10.008
129. Mahe, P., & Vert, J. P. (2009). Graph kernels based on tree patterns for molecules. Machine Learning, 75(1), 3-35. doi:10.1007/s10994-008-5086-2
130. Martin, Y. C., & Willett, P. (1998). Designing bioactive molecules. Three-dimensional techniques and applications. Washington, D.C.: American Chemical Society.
131. Rupp, M., & Schneider, G. (2010). Graph kernels for molecular similarity. Molecular Informatics, 29(4), 266-273.
132. Schietgat, L., Ramon, J., Bruynooghe, M., & Blockeel, H. (2008). An efficiently computable graph-based metric for the classification of small molecules. Discovery Science. Proceedings, 5255, 197-209.
133. Smith, G. R., & Sternberg, M. J. E. (2002). Prediction of protein-protein interactions by docking methods. Current Opinion in Structural Biology, 12(1), 28-35. doi:10.1016/S0959-440X(02)00285-3
134. Trinajstic, I. (1983). Chemical Graph Theory. Chichester: Ellis Horwood.
135. Willett, P. (2005). Searching techniques for databases of two-and three-dimensional chemical structures. Journal of Medicinal Chemistry, 48(13), 4183-4199. doi:10.1021/jm0582165
136. Willett, P. (2008). From chemical documentation to chemoinformatics: 50 years of chemical information science. Journal of Information Science, 34(4), 477-499. doi:10.1177/0165551507084631
137. Willett, P., Barnard, J. M., & Downs, G. M. (1998). Chemical similarity searching. Journal of Chemical Information and Computer Sciences, 38(6), 983-996. doi:10.1021/ci9800211