Quantifying the fingerprint descriptor dependence of structure-activity relationship information on a large scale

Journal of Chemical Information and Modeling

Volumn 53, Issue 9, 2013, Pages 2275-2281

  Dimova, Dilyana ^a   Stumpfe, Dagmar ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

ACTIVE COMPOUNDS; HIGH CONFIDENCE; MOLECULAR REPRESENTATIONS; MOLECULAR SIMILARITY; NUMERICAL RESULTS; PHARMACOPHORES; STRUCTURE ACTIVITY RELATIONSHIPS; SYSTEMATIC ANALYSIS;

PALMPRINT RECOGNITION;

MOLECULAR LIBRARY;

BIOLOGY; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR LIBRARY; PROCEDURES; STRUCTURE ACTIVITY RELATION; ARTICLE; METHODOLOGY;

COMPUTATIONAL BIOLOGY; HUMANS; SMALL MOLECULE LIBRARIES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84884546172     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci4004078     Document Type: Article

References (24)

1. Wermuth, C. G. The Practice of Medicinal Chemistry, 3 rd ed.; Academic Press: Waltham, MA, 2008.
2. Wawer, M.; Lounkine, E.; Wassermann, A. M.; Bajorath, J. Data Structures and Computational Tools for the Extraction of SAR Information from Large Compound Sets Drug Discovery Today 2010, 15, 631-639
3. 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
4. Stumpfe, D.; Bajorath, J. Methods for SAR Visualization RSC Adv. 2012, 2, 369-378
5. Peltason, L.; Bajorath, J. SAR Index: Quantifying the Nature of Structure-Activity Relationships J. Med. Chem. 2007, 50, 5571-5578
6. Guha, R.; Van Drie, J. H. Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs J. Chem. Inf. Model. 2008, 48, 646-658
7. Kubinyi, H. Similarity and Dissimilarity: A Medicinal Chemist's View Perspect. Drug Discovery Des. 1998, 9-11, 225-232
8. Concepts and Applications of Molecular Similarity; Johnson, M. A.; Maggiora, G. M., Eds.; John Wiley & Sons: New York, 1990.
9. Eckert, H.; Bajorath, J. Molecular Similarity Analysis in Virtual Screening: Foundations, Limitations and Novel Approaches Drug Discovery Today 2007, 12, 225-233
10. Willett, P. Searching Techniques for Databases of Two-and Three-Dimensional Structures J. Med. Chem. 2005, 48, 4183-4199
11. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching J. Chem. Inf. Comput. Sci. 1998, 38, 983-996
12. Stumpfe, D.; Bajorath, J. Similarity Searching Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 260-282
13. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. Scaffold-Hopping by Topological Pharmacophore Search: A Contribution to Virtual Screening Angew. Chem., Int. Ed. 1999, 19, 2894-2896
14. Wassermann, A. M.; Wawer, M.; Bajorath, J. Activity Landscape Representations for Structure-Activity Relationship Analysis J. Med. Chem. 2010, 53, 8209-8223
15. Maggiora, G. M. On Outliers and Activity Cliffs-Why QSAR Often Disappoints J. Chem. Inf. Model. 2006, 46, 1535-1535
16. Stumpfe, D.; Bajorath, J. Exploring Activity Cliffs in Medicinal Chemistry J. Med. Chem. 2012, 55, 2932-2942
17. Medina-Franco, J. L.; Martínez-Mayorga, K.; Bender, A.; Marín, R. M.; Giulianotti, M. A.; Pinilla, C.; Houghten, R. A. Characterization of Activity Landscapes using 2D and 3D Similarity Methods: Consensus Activity Cliffs J. Chem. Inf. Model. 2009, 49, 477-491
18. Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. P. ChEMBL: A Large-scale Bioactivity Database for Drug Discovery Nucleic Acids Res. 2011, 40, D1100-D1107
19. Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
20. MACCS Structural Keys; Accelrys: San Diego, CA.
21. Molecular Operating Environment (MOE); Chemical Computing Group Inc.: Montreal, Quebec, Canada.
22. Peltason, L.; Hu, Y.; Bajorath, J. From Structure-Activity to Structure-Selectivity Relationships: Quantitative Assessment, Selectivity Cliffs, and Key Compounds ChemMedChem. 2009, 4, 1864-1873
23. 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
24. Vogt, M.; Stumpfe, D.; Geppert, H.; Bajorath, J. Scaffold Hopping Using Two-dimensional Fingerprints: True Potential, Black Magic, or a Hopeless Endeavor? Guidelines for Virtual Screening J. Med. Chem. 2010, 53, 5707-5715