A similarity-based data-fusion approach to the visual characterization and comparison of compound databases

Chemical Biology and Drug Design

Volumn 70, Issue 5, 2007, Pages 393-412

  Medina Franco, José L ^a,b   Maggiora, Gerald M ^a   Giulianotti, Marc A ^b   Pinilla, Clemencia ^b   Houghten, Richard A ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b TORREY PINES INSTITUTE FOR MOLECULAR STUDIES   (United States)

Author keywords

Combinatorial libraries; Compound acquisition; Compound selection; Data visualization; Diversity analysis; Fusion based similarity; Ligand based virtual screening; Multi fusion similarity maps

Indexed keywords

ANALYTIC METHOD; ARTICLE; CHEMICAL ANALYSIS; DATA ANALYSIS; DATA BASE; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SCREENING; VIRTUAL SCREENING;

COMBINATORIAL CHEMISTRY TECHNIQUES; DATABASES, FACTUAL; DRUG DESIGN; MODELS, MOLECULAR; MOLECULAR CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 35348970306     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2007.00579.x     Document Type: Article

References (61)

1. Scior T., Bernard P., Medina-Franco J.L., Maggiora G.M. (2007) Large compound databases for structure-activity relationships in drug discovery. Mini Rev Med Chem 7: 851 860.
2. Leach A.R., Gillet V.J. (2007) An Introduction to Chemoinformatics (revised edition). New York: Springer.
3. Baldi P. (2005) Chemoinformatics, drug design, and systems biology. Genome Inform 16: 281 285.
4. Oprea T.I., Gottfries J. (2001) Chemography: the art of navigating in chemical space. J Comb Chem 3: 157 166.
5. Aleksandrov A.D., Kolmogorov A.N., Laurent've M.A. (1986) Mathematics - Its Content, Methods, and Meaning, Volume 3 (Translated by K, Hirsch). Cambridge, Massachusetts: The MIT Press.
6. Todeschinin R., Consonni V. (2002) Handbook of Molecular Descriptors. Weinheim, Germany: Wiley-VCH Verlag GmbH.
7. Maggiora G.M., Shanmugasundaram V. (2004) Molecular Similarity Measures. In: Bajorath J., editor. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery. Totowa, New Jersey: Humana Press p. 1 50.
8. Carbó R., Calabuig B. (1990) Molecular similarity and quantum chemistry. In: Johnson M.A., Maggiora G.M., editors. Concepts and Applications of Molecular Similarity. New York: John Wiley & Sons p. 147 171.
9. Jolliffe I.T. (2002) Principal Component Analysis, 2nd edn. New York: Springer.
10. Borg I., Groenen P. (1997) Modern Multidimensional Scaling - Theory and Applications. New York: Springer.
11. Rassokhin D.N., Lobanov V.S., Agrafiotis D.K. (2001) Nonlinear mapping of massive data sets by fuzzy clustering and neural networks. J Comput Chem 22: 373 386.
12. Agrafiotis D.K. (2003) Stochastic proximity embedding. J Comp Chem 24: 1215 1221.
13. Pearlman R.S., Smith K.M. (1998) Novel software tools for chemical diversity. Perspect Drug Discov Des 9: 339 353.
14. Agrafiotis D.K., Rassokhin D.N. (2002) A fractal approach to selecting an appropriate bin size for cell-based diversity estimation. J Chem Inf Comput Sci 42: 117 122.
15. Xue L., Bajorath J. (2002) Accurate portioning of compounds belonging to diverse activity classes. J Chem Inf Comput Sci 42: 757 764.
16. Xue L., Stahura F.L., Bajorath J. (2004) Cell-Base Partitioning. In: Bajorath J., editor. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery. New Jersey: Humana Press, Totowa p. 279 289.
17. Rush J.A. (1999) Cell-based methods for sampling in high-dimensional spaces. In: Truhlar D.G., Howe W.J., Hopfinger A.J., Blaney J., Dammkoehler R.A., editors. Rational Drug Design. New York: Springer p. 73 79.
18. Lam R.L.H., Welch W.J., Young S.S. (2005) Cell-based Binning Methods and Cell Coverage System for Molecule Selection. US Patent Number 6850876, Issued 1 February 2005. Assignee: Smithkline Beecham.
19. Maggiora G.M., Shanmugasundaram V., Lajiness M.S., Doman T.N., Schultz M.W. (2005) A practical strategy for directed compound acquisition. In: Oprea T.I., editor. Chemoinformatics in Drug Discovery. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA p. 317 332.
20. Downs G.M., Barnard J.M. (2002) Clustering methods and their uses in computational chemistry. Rev Comput Chem 18: 1 40.
21. Holliday J.D., Rogers S.L., Willett P., Chen M., Madfouf M., Lawson K., Mullier G. (2004) Clustering files of chemical structures using the fuzzy k-means clustering method. J Chem Inf Comput Sci 44: 894 902.
22. Böcker A., Dersen S., Schmidt E., Teckentrup A., Schneider G. (2005) A hierarchical clustering approach for large compound libraries. J Chem Inf Model 45: 807 815.
23. Böcker A., Schneider G., Teckentrup A. (2006) NIPALSTREE: a new hierarchical clustering approach for large compound libraries and its application to virtual screening. J Chem Inf Model 46: 2220 2229.
24. Brewer M.L. (2007) Development of a spectral clustering method for the analysis of molecular data sets. J Chem Inf Model 47: 1727 1733.
25. Carhart R.E., Smith D.H., Venkataraghavan R. (1985) Atom pairs as molecular-features in structure-activity studies - definition and applications. J Chem Inf Comput Sci 25: 64 73.
26. Willett P., Winterman V., Bawden D. (1986) Implementation of nearest-neighbor searching in an online chemical structure search system. J Chem Inf Comput Sci 26: 36 41.
27. Hert J., Willett P., Wilton D.J., Acklin P., Azzaoui K., Jacoby E., Schuffenhauer A. (2005) Enhancing the effectiveness of similarity-based virtual screening using nearest-neighbor information. J Med Chem 48: 7049 7054.
28. Dutta D., Guha R., Jurs P., Chen T. (2006) Scalable partitioning and exploration of chemical spaces using geometric hashing. J Chem Inf Model 46: 321 333.
29. Guha R., Dutta D., Jurs P., Chen T. (2006) R-NN curves: an intuitive approach to outlier detection using a distance based method. J Chem Inf Model 46: 1713 1722.
30. Shanmugasundaram V., Maggiora G.M., Lajiness M.S. (2005) Hit-directed nearest-neighbor searching. J Med Chem 48: 240 248.
31. Agrafiotis D.K. (1997) On the use of information theory for assessing molecular diversity. J Chem Inf Comput Sci 37: 576 580.
32. Yan A. (2006) Application of self-organizing maps in compound pattern recognition and combinatorial library design. Comb Chem High Throughput Screen 9: 473 480.
33. Sheridan R.P., Kearsley S.K. (2002) Why do we need so many chemical similarity search methods? Drug Discov Today 7: 903 911.
34. Ginn C.M.R., Willett P., Bradshaw J. (2000) Combination of molecular similarity measures using data fusion. Perspect Drug Discov Des 20: 1 16.
35. Hert J., Willet P., Wilton D.J. (2004) Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. J Chem Inf Comput Sci 44: 1177 1185.
36. Willett P. (2005) Searching techniques for databases of two- and three-dimensional chemical structures. J Med Chem 48: 4183 4199.
37. Willett P. (2006) Similarity-based virtual screening using 2D fingerprints. Drug Discovery Today 11: 1046 1053.
38. Hall D.L., McMullen S.A.H. (2004) Mathematical Techniques in Multisensor Data Fusion, 2nd edn. Norwood, Massachusetts: Artech House.
39. Klein L.A. (2004) Sensor and Data Fusion: A Tool for Information Assessment and Decision Making. Bellingham: SPIE Press.
40. Xue L., Stahura F.L., Godden J.W., Bajorath J. (2001) Fingerprint scaling increases the probability of identifying molecules with similar activity in virtual screening calculations. J Chem Inf Comput Sci 41: 746 753.
41. Schuffenhauer A. (2003) Similarity metrics for ligands reflecting the similarity of target proteins. J Chem Inf Comput Sci 43: 391 405.
42. Hert J., Willett P., Wilton D.J., Acklin P., Azzaoui K., Jacoby E., Schuffenhauer A. (2006) New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching. J Chem Inf Model 46: 462 470.
43. Truchon J.-F., Bayly C.I. (2007) Evaluating virtual screening method: good and bad metrics for the "early recognition" problem. J Chem Inf Model 47: 488 508.
44. Williams C. (2006) Reverse fingerprinting, similarity searching by group fusion and fingerprint bit importance. Mol Divers 10: 311 332.
45. Tovar A., Eckert H., Bajorath J. (2007) Comparison of 2D fingerprint methods for multiple-template similarity searching on compound activity classes of increasing structural diversity. Chem Med Chem 2: 208 217.
46. Wishart D.S., Knox C., Guo A.C., Shrivastava S., Hassanali M., Stothard P., Chang Z., Woolsey J. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 34: D668 D672.
47. Olah M., Mracec M., Ostopovici L., Rad R., Bora A., Hadaruga N., Olah I., Banda M., Simon Z., Mracec M., Oprea T.I. (2004) WOMBAT: world of molecular bioactivity. In: Oprea T.I., editor. Chemoinformatics in Drug Discovery. New York: Wiley-VCH p. 221 239.
48. Willett P., Barnard J.P., Downs G.M. (1998) Chemical similarity searching. J Chem Inf Comput Sci 38: 983 996.
49. Flower D.R. (1998) On the properties of bit-string based measures of chemical similarity. J Chem Inf Comput Sci 38: 379 386.
50. Holliday J.D., Salim N., Whittle M., Willett P. (2003) Analysis and display of size dependence of chemical similarity coefficients. J Chem Inf Comput Sci 43: 819 828.
51. Liu T., Lin Y., Wen X., Jorissen R.N., Gilson M.K. (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 35: D198 D201.
52. Kearsley S.K., Sallamack S., Fluder E.M., Andose J.D., Mosley R.T., Sheridan R.P. (1996) Chemical similarity using physiochemical property descriptors. J Chem Inf Comput Sci 36: 118 127.
53. Ginn C.M.R., Turner D.B., Willett P., Freguson A.M., Heritage T.W. (1997) Similarity searching in files of three-dimensional chemical structures: evaluation of the EVA descriptor and combination of rankings using data fusion. J Chem Inf Comput Sci 37: 23 37.
54. Lootsma F.A. (1999) Multi-Criteria Decision Analysis via Ratio and Difference Judgement. Dordrecht, The Netherlands: Kluwer Academic Publishers.
55. Gillet V.J., Willett P., Fleming P.J., Green D.V.S. (2002) Design focused libraries using MoSELECT. J Mol Graph Model 20: 491 498.
56. Agrafiotis D.K. (2002) Multiobjective optimization of combinatorial libraries. J Comput Aided Mol Des 16: 335 356.
57. Gillet V.J. (2004) Applications of evolutionary computation in drug design. In: Johnston R.L., editor. Applications of Evolutionary Computation in Chemistry. New York: Springer p. 133 152.
58. Soltanshahi F., Mansley T.E., Choi S., Clark R.D. (2006) Balancing focused combinatorial libraries based on multiple GPCR ligands. J Comput Aided Mol Des 20: 529 538.
59. Lajiness M.S. (1997) Dissimilarity-based compound selection techniques. Perspect Drug Discov Des 7/8: 65 84.
60. Irwin J.J., Shoichet B.K. (2005) Zinc - a free database of commercially available compounds for virtual screening. J Chem Inf Model 45: 177 182.
61. Deb K. (2001) Multi-Objective Optimization using Evolutionary Optimization. New York: John Wiley & Sons.