Representing clusters using a maximum common edge substructure algorithm applied to reduced graphs and molecular graphs

Journal of Chemical Information and Modeling

Volumn 47, Issue 2, 2007, Pages 354-366

  Gardiner, Eleanor J ^a   Gillet, Valerie J ^a   Willett, Peter ^a   Cosgrove, David A ^b  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b ASTRAZENECA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; CONFORMAL MAPPING; DATABASE SYSTEMS; EDGE DETECTION; FUNCTIONAL GROUPS; GRAPHIC METHODS;

CHEMICAL DATABASES; MAXIMUM COMMON EDGE SUBSTRUCTURE (MCES) ALGORITHMS; MOLECULAR GRAPHS;

CLUSTER ANALYSIS;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CLUSTER ANALYSIS;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; MOLECULAR STRUCTURE;

EID: 34247257243     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600444g     Document Type: Article

References (27)

1. Lajiness, M. S.; Maggiora, G. M.; Shanmugasundaram, V. Assessment of the Consistency of Medicinal Chemists in Reviewing Sets of Compounds. J. Med. Chem. 2004, 47, 4891-4896.
2. Raymond, J. W.; Gardiner, E. J.; Willett, P. Heuristics for Similarity Searching of Chemical Graphs Using a Maximum Common Edge Subgraph Algorithm. J. Chem. Inf. Comput. Sci. 2002, 42, 305-316.
3. Stahl, M.; Mauser, H.; Tsui, M.; Taylor, N. R. A Robust Clustering Method for Chemical Structures. J. Med. Chem. 2005, 48, 4358-4366.
4. Wilkens, S. J.; Janes, J.; Su, A. I. HierS: Hierarchical Scaffold Clustering Using Topological Chemical Graphs. J. Med. Chem. 2005, 48, 3182-3193.
5. Wolohan, P. R. N.; Akella, L. B.; Dorfman, R. J.; Nell, P. G.; Mundt, S. M.; Clark, R. D. Structural Unit Analysis Identifies Lead Series and Facilitates Scaffold Hopping in Combinatorial Chemistry. J. Chem. Inf. Model. 2006, 46, 1188-1193.
6. Stahl, M.; Mauser, H. Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods. J. Chem. Inf. Model. 2005, 45, 542-548.
7. Butina, D. Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way to Cluster Small and Large Data Sets. J. Chem. Inf. Comput. Sci. 1999, 39, 747-750.
8. Raymond, J. W.; Kibbey, C. E. An Automated Method for Exploring Targeted Substructural Diversity within Sets of Chemical Structures. J. Chem. Inf. Model. 2005, 45, 1195-1204.
9. Barker, E. J. Chemical Similarity Searching Using Reduced Graphs. Ph.D. Thesis, University of Sheffield, Sheffield, United Kingdom, 2004.
10. Barker, E. J.; Gardiner, E. J.; Gillet, V. J.; Kitts, P.; Morris, J. Further Development of Reduced Graphs for Identifying Bioactive Compounds. J. Chem. Inf. Comput. Sci. 2003, 43, 346-356.
11. Gillet, V. J.; Willett, P.; Bradshaw, J. Similarity Searching Using Reduced Graphs. J. Chem. Inf. Camput. Sci. 2003, 43, 338-345.
12. Birchall, K.; Gillet, V. J.: Harper, G.; Pickett. S. D. Training Similarity Measures for Specific Activities: Application to Reduced Graphs. J, Chem. Inf. Model. 2006, 46, 577-586.
13. Barker, E. J.; Buttar, D.; Cosgrove, D. A.; Gardiner, E. J.; Kitts, P.; Willett, P.; Gillet, V. J. Scaffold Hopping Using Clique Detection Applied to Reduced Graphs. J. Chem. Inf. Model. 2006, 46, 503-511.
14. Rarey, M.; Dixon, J. S. Feature Trees: A New Molecular Similarity Measure Based on Tree Matching. J. Comput.-Aided Mol. Des. 1998, 12 (5), 471-490.
15. Harper, G.; Bravi, G. S.; Pickett, S. D.; Hussain, J.; Green. D. V. S. The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data. J. Chem. Inf. Comput. Sci. 2004, 44, 2145-2156.
16. Takahashi, Y.; Sukekawa, M.; Sasaki, S. Automatic Identification of Molecular Similarity Using Reduced-Graph Representation of Chemical-Structure. J. Chem. Inf. Comput. Sci. 1992, 32, 639-643.
17. MDL; MDL Information Systems, Inc.: San Leandro, CA. http://www.mdli.com (accessed Nov 30 2006).
18. Figueras, J. Ring Perception Using Breadth-First Search. J. Chem. Inf. Comput. Sci. 1996, 36, 986-991.
19. OEchem; OpenEye Scientific Software, Santa Fe, NM. http://www.eyesopen.com (accessed Nov 30 2006).
20. Davis, A. M.; Keeling, D. J.; Steele, J.; Tomkinson, N. P.; Tinker, A. C. Components of Successful Lead Generation. Curr. Top. Med. Chem. 2005, 5, 421-439.
21. Daylight Chemical Information Systems, Inc.. Los Altos. CA. http://www.daylight.com (accessed Nov 30 2006).
22. Matlab, version 7.1; The Mathworks, Inc.: Novi, MI. http://www.mathworks.com (accessed Nov 30 2006).
23. Raymond, J. W.; Gardiner, E. J.; Willett, P. RASCAL: Calculation of Graph Similarity Using Maximum Common Edge Subgraphs. Comput. J. 2002, 45, 631-644.
24. Raymond, J. W.; Willett, P. Maximum Common Subgraph Isomorphism Algorithms for the Matching of Chemical Structures. J. Comput.-Aided Mol Des. 2002, 16, 521-533.
25. J. D. Alert Database; Current Drugs Ltd.: London, U. K.
26. Qt, version 4.1; Trolltech: Oslo, Norway, http://www.trolltech.com (accessed Nov 30 2006).
27. Kibbey, C.; Calvet, A. Molecular Property eXplorer: A Novel Approach to Visualizing SAR Using Tree-Maps and Heatmaps. J. Chem. Inf. Model 2005, 45, 523-532.