SAR monitoring of evolving compound data sets using activity landscapes

Journal of Chemical Information and Modeling

Volumn 51, Issue 3, 2011, Pages 532-540

  Iyer, Preeti ^a   Hu, Ye ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ANALYSIS; ESSENTIAL OILS; SCAFFOLDS;

ACTIVE COMPOUNDS; COMPOUND COLLECTIONS; INFORMATION CONTENTS; ITERATIVE PROCESS; PHARMACEUTICAL RESEARCH; SMALL MOLECULES; STRUCTURE-ACTIVITY RELATIONSHIPS; THERAPEUTIC TARGETS;

MONITORING;

ARTICLE; CHEMICAL STRUCTURE; DRUG DEVELOPMENT; MOLECULAR LIBRARY; STRUCTURE ACTIVITY RELATION;

DRUG DISCOVERY; MODELS, MOLECULAR; SMALL MOLECULE LIBRARIES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79953199464     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100505m     Document Type: Article

References (24)

1. Peltason, L.; Bajorath, J. Systematic computational analysis of structure-activity relationships: Concepts, challenges and recent advances Future Med. Chem. 2009, 1, 451-466
2. Esposito, E. X.; Hopfinger, A. J.; Madura, J. D. Methods for applying the quantitative structure-activity relationship paradigm Methods Mol. Biol. 2004, 275, 131-214
3. Leach, A. R.; Gillet, V. J.; Lewis, R. A.; Taylor, R Three-dimensional pharmacophore methods in drug discovery J. Med. Chem. 2010, 53, 539-558
4. Nicholls, A.; McGaughey, G. B.; Sheridan, R. P.; Good, A. C.; Warren, G.; Mathieu, M.; Muchmore, S. W.; Brown, S. P.; Grant, J. A.; Haigh, J. A.; Nevins, N.; Jain, A. N.; Kelley, B. Molecular shape and medicinal chemistry: A perspective J. Med. Chem. 2010, 53, 3862-3886
5. Geppert, H.; Vogt, M.; Bajorath, J. Current trends in ligand-based virtual screening: Molecular representations, data mining methods, new application areas, and performance evaluation J. Chem. Inf. Model. 2010, 50, 205-216
6. Ahlberg, C. Visual exploration of HTS databases: Bridging the gap between chemistry and biology Drug Discovery Today 1999, 4, 370-376 (Pubitemid 29457487)
7. Roberts, G.; Myatt, G. J.; Johnson, W. P.; Cross, K. P.; Blower, P. E., Jr. LeadScope: Software for exploring large sets of screening data J. Chem. Inf. Comput. Sci. 2000, 40, 1302-1314
8. Wawer, M.; Peltason, L.; Bajorath, J. Elucidation of structure-activity relationship pathways in biological screening data J. Med. Chem. 2009, 52, 1075-1080
9. Wassermann, A. M.; Wawer, M.; Bajorath, J. Activity landscape representations for structure-activity relationship analysis J. Med. Chem. 2010, 53, 8209-8223
10. Peltason, L.; Bajorath, J. SAR Index: Quantifying the nature of structure-activity relationships J. Med. Chem. 2007, 50, 5571-5578 (Pubitemid 350106013)
11. Wawer, M.; Peltason, L.; Weskamp, N.; Teckentrup, A.; Bajorath, J. Structure-activity relationship anatomy by network-like similarity graphs and local structure-activity relationship indices J. Med. Chem. 2008, 51, 6075-6084
12. Peltason, L.; Iyer, P.; Bajorath, J. Rationalizing three-dimensional activity landscapes and the influence of molecular representations on landscape topology and the formation of activity cliffs J. Chem. Inf. Model. 2010, 50, 1021-1033
13. ChEMBL; European Bioinformatics Institute (EBI): Cambridge, 2010. http://www.ebi.ac.uk/chembl/ (accessed November 02, 2010).
14. Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1. Molecular frameworks J. Med. Chem. 1996, 39, 2887-2893 (Pubitemid 26251026)
15. SciTegic's Pipeline Pilot, Student ed., version 6.1; Accelrys, Inc.: San Diego, 2007.
16. Willett, P. Searching techniques for databases of two- and three-dimensional structures J. Med. Chem. 2005, 48, 1-17
17. MACCS Structural Keys; Symyx Software: San Ramon, CA, 2005.
18. Maggiora, G. M. On outliers and activity cliffs: Why QSAR often disappoints J. Chem. Inf. Model. 2006, 46, 1535-1535
19. Fruchterman, T. M. J.; Reingold, E. M. Graph drawing by force-directed placement Software-Pract. Exper. 1991, 21, 1129-1164
20. Csardi, G. The igraph library, version 0.5.5; Budapest, Hungary, 2009., http://igraph.sourceforge.net/ (accessed December 16, 2010).
21. R: A Language and Environment for Statistical Computing; R Development Core Team, R Foundation for Statistical Computing: Vienna, Austria, 2010.
22. Borg, I.; Groenen, P.J. F. Modern Multidimensional Scaling. Theory and Applications, 2 nd ed.; Springer: New York, 2005.
23. Cressie, N. Statistics for Spatial Data, revised ed.; Wiley: New York, 1993.
24. Furrer, R.; Nychka, D.; Sain, S. Tools for Spatial Data, R Package, version 6.30; R Foundation for Statistical Computing: Vienna, Austria, 2009.