Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2

Journal of Cheminformatics

Volumn 4, Issue 7, 2012, Pages

  Ehrlich, Hans Christian ^a   Rarey, Matthias ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Algorithm; Benchmark; SMARTS; Subgraph isomorphism; Substructure search

Indexed keywords

EID: 84867453935     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-4-13     Document Type: Article

References (42)

1. Irwin J, Shoichet B: ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 2005, 45:177-182. (Pubitemid 40736970)
2. Bolton EE, Wang Y, Thiessen PA, Bryant SH: Chapter 12 PubChem: Integrated Platform of Small Molecules and Biological Activities. In Annual Reports in Computational Chemistry Volume 4, Volume 4 of Annual Reports in Computational Chemistry. Edited by Wheeler RA, Spellmeyer DC. Elsevier; 2008:217-241. [http://www.sciencedirect.com/science/article/pii/S1574140008000121].
3. Sussenguth EH: A graph-theoretic algorithm for matching chemical Structures. J Chem Documentation 1965, 5:36-43. [http://pubs.acs.org/doi/abs/10. 1021/c160016a007].
4. Figueras J: Substructure search by set reduction. J Chem Documentation 1972, 12(4):237-244. [http://pubs.acs.org/doi/abs/10.1021/c160047a010].
5. Read RC, Corneil DG: The graph isomorphism disease. J Graph Theory 1977, 1(4):339-363. [http://dx.doi.org/10.1002/jgt.3190010410].
6. Gati G: Further annotated bibliography on the isomorphism disease. J Graph Theory 1979, 3(2):95-109. [http://dx.doi.org/10.1002/jgt.3190030202].
7. Ullmann JR: An algorithm for subgraph isomorphism. J Assoc Comput Mach 1976, 23:31-42.
8. Attias R: DARC substructure search system: a new approach to chemical information. J Chem Inf Comput Sci 1983, 23(3):102-108. [http://pubs.acs.org/ doi/abs/10.1021/ci00039a003]. (Pubitemid 14452176)
9. Heyman J, Karasinskia E, Giles P: CAS information services for medicinal chemists. Drug Inf J 1982, 16(4):185-190.
10. Willett P, Barnard JM, Downs GM: Chemical similarity searching. J Chem Inf Model 1998, 38(6):983-996. [http://dx.doi.org/10.1021/ci9800211]. (Pubitemid 128591261)
11. Cordella L, Foggia P, Sansone C, Vento M: Performance evaluation of the VF graph matching algorithm. In Image Analysis and Processing, 1999. Proceedings. International Conference on. 1999:1172-1177.
12. Cordella LP, Foggia P, Sansone C, Vento M: A (sub) graph isomorphism algorithm for matching large graphs. IEEE Trans Pattern Anal Machine Intelligence 2004, 26(10):1367-1372.
13. Yan X, Yu PS, Han J: Substructure similarity search in graph databases. In Proceedings of the 2005 ACM SIGMOD international conference on Management of data, SIGMOD'05. New York, NY, USA: ACM; 2005:766-777. [http://doi.acm.org/10. 1145/1066157.1066244]. (Pubitemid 43038974)
14. Golovin A, Henrick K: Chemical substructure search in SQL. J Chem Inf Model 2009, 49:22-27.
15. Willett P, Wilson T, Reddaway SF: Atom-by-atom searching using massive parallelism. Implementation of the Ullmann subgraph isomorphism algorithm on the distributed array processor. J Chem Inf Comput Sci 1991, 31(2):225-233. [http://pubs.acs.org/doi/abs/10.1021/ci00002a008].
16. Messmer BT: Efficient Graph Matching Algorithms 1995.
17. Foggia P, Sansone C, Vento M: A performance comparison of five algorithms for graph isomorphism. Proc of the 3rd IAPR TC-15 Workshop on Graph-based Representations in Pattern Recognition. 2001:188-199.
18. Brint AT, Willett P: Algorithms For the Identification of 3-dimensional Maximal Common Substructures. J Chem Inf Comput Sci 1987, 27(4):152-158. (Pubitemid 18534851)
19. Downs GM, Lynch MF, Willett P, Manson GA, Wilson GA: Transputer implementations of chemical substructure searching algorithms. Tetrahedron Comput Methodology 1988, 1(3):207-217. [http://dx.doi.org/10.1016/0898-5529(88) 90026-7].
20. Barnard JM: Substructure searching methods: old and new. J Chem Inf Comput Sci 1993, 33(4):532-538. [http://pubs.acs.org/doi/abs/10.1021/ ci00014a001].
21. Oprea TI: Chemoinformatics in drug discovery. Weinheim: Wiley-VCH; 2005:76-79. chap. 4.4.2.1.
22. Agrafiotis DK, Lobanov VS, Shemanarev M, Rassokhin DN, Izrailev S, Jaeger EP, Alex S, Farnum M: Efficient substructure searching of large chemical libraries: the ABCD chemical cartridge. J Chem Inf Model 0, 0 (0):null. [http://pubs.acs.org/doi/abs/10.1021/ci200413e].
23. Falkenhainer B, Forbus KD, Gentner D: The structure-mapping engine: algorithm and examples. Artif Intelligence 1989, 41:1-63.
24. Tarjan RE: Graph Algorithms in Chemical Computation. American Chemical Society; 1977:1-20. chap. 2, [http://pubs.acs.org/doi/abs/10.1021/bk-1977-0046. ch001].
25. Ash S, Cline MA, Homer RW, Hurst T, Smith GB: SYBYL line notation (SLN): A versatile language for chemical structure representation. J Chem Inf Comput Sci 1997, 37:71-79. (Pubitemid 127601580)
26. Koniver DA, Wiswesser WJ, Usdin E: Wiswesser line notation: simplified techniques for converting chemical structures to WLN. Science 1972, 176(4042):1437-1439. [http://dx.doi.org/10.1126/science.176.4042.1437].
27. Hann M, Hudson B, Lewell X, Lifely R, Miller L, Ramsden N: Strategic pooling of compounds for high-throughput screening. J Chem Inf Comput Sci 1999, 39(5):897-902. [http://pubs.acs.org/doi/abs/10.1021/ci990423o].
28. Walters W, Murcko MA: Prediction of 'drug-likeness'. Adv Drug Delivery Rev 2002, 54(3):255-271. [http://www.sciencedirect.com/science/article/pii/ S0169409X02000030]. [Computational Methods for the Prediction of ADME and Toxicity].
29. Abolmaali S F B, Wegner JK, Zell A: The compressed feature matrix - a fast method for feature based substructure search. J Mol Model 2003, 9:235-241. [http://dx.doi.org/10.1007/s00894-003-0126-0]. [10.1007/s00894-003-0126-0]. (Pubitemid 37240065)
30. Olah M, Bologa C, Oprea TI: An automated PLS search for biologically relevant QSAR descriptors. J Comput Aided Mol Des 2004, 18:437-449. [http://dx.doi.org/10.1007/s10822-004-4060-8]. [10.1007/s10822-004-4060-8].
31. Maass P, Schulz-Gasch T, Stahl M, Rarey M: Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations. J Chem Inf Model 2007, 47(2):390-399. [http://pubs.acs.org/doi/ abs/10.1021/ci060094h]. [PMID: 17305328]. (Pubitemid 46615943)
32. Agrafiotis DK, Gibbs AC, Zhu F, Izrailev S, Martin E: Conformational sampling of bioactive molecules: a comparative study. J Chem Inf Model 2007, 47(3):1067-1086. [http://pubs.acs.org/doi/abs/10.1021/ci6005454]. [PMID: 17411028]. (Pubitemid 46973722)
33. Enoch, S J, Madden, J C, Cronin, M T D: Identification of mechanisms of toxic action for skin sensitisation using a SMARTS pattern based approach. SAR QSAR Environ Res 2008, 19(5-6):555-578. [http://dx.doi.org/10.1080/ 10629360802348985].
34. Baell JB, Holloway GA: New substructure filters for removal of Pan Assay Interference Compounds (PAINS) from screening libraries and for their exclusion in Bioassays. J Med Chem 2010, 53(7):2719-2740. [http://pubs.acs.org/doi/abs/10. 1021/jm901137j]. [PMID: 20131845].
35. Ihlenfeldt WD, Takahashi Y, Abe H, ichi Sasaki S: Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and compatibility. J Chem Inf Comput Sci 1994, 34:109-116.
36. Xu J: GMA: a generic match algorithm for structural homomorphism, isomorphism, and maximal common substructure match and its applications. J Chem Inf Comput Sci 1996, 36:25-34. [http://pubs.acs.org/doi/abs/10.1021/ci950061u]. (Pubitemid 126579130)
37. Gasteiger J, Engel T (Eds): Chemoinformatics: A Textbook. 1 edition. Wiley-VCH; 2003. [http://www.worldcat.org/isbn/3527306811].
38. Schomburg K, Ehrlich HC, Stierand K, Rarey M: From structure diagrams to visual chemical patterns. J Chem Inf Model 2010, 50(9):1529-1535. [http://dx.doi.org/10.1021/ci100209a].
39. Ozawa K, Yasuda T, Fujita S: Substructure search with tree-structured data. J Chem Inf Comput Sci 1997, 37(4):688-695. [http://pubs.acs.org/doi/abs/ 10.1021/ci960378%2B]. (Pubitemid 127603580)
40. Rughooputh S D D V, Rughooputh H C S: Neural network based chemical structure indexing. J Chem Inf Comput Sci 2001, 41(3):713-717. [http://pubs.acs.org/doi/abs/10.1021/ci000394d].
41. Miller MA: Chemical database techniques in drug discovery. Nat Rev Drug Discov 2002, 1(3):220-227. [http://dx.doi.org/10.1038/nrd745]. (Pubitemid 37361425)
42. Jeliazkova N, Kochev N: AMBIT-SMARTS: efficient searching of chemical structures and fragments. Mol Informatics 2011, 30(8):707-720. [http://dx.doi.org/10.1002/minf.201100028].