Multiobjective particle swarm optimization: Automated identification of structure - Activity relationship-informative compounds with favorable physicochemical property distributions

Journal of Chemical Information and Modeling

Volumn 52, Issue 11, 2012, Pages 2848-2855

  Namasivayam, Vigneshwaran ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PARETO PRINCIPLE; PARTICLE SWARM OPTIMIZATION (PSO); PHYSICOCHEMICAL PROPERTIES; STRUCTURES (BUILT OBJECTS);

ACTIVE COMPOUNDS; AUTOMATED IDENTIFICATION; CHEMICAL OPTIMIZATIONS; LARGE DATASETS; MULTI OBJECTIVE PARTICLE SWARM OPTIMIZATION; MULTIPLE-OBJECTIVES; PARETO OPTIMIZATION; STRUCTURE-ACTIVITY RELATIONSHIPS;

MULTIOBJECTIVE OPTIMIZATION;

ENZYME INHIBITOR;

ALGORITHM; ANIMAL; ARTICLE; CHEMISTRY; DRUG DATABASE; HUMAN; METABOLISM; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; ANIMALS; DATABASES, PHARMACEUTICAL; ENZYME INHIBITORS; HUMANS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84870037364     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300402g     Document Type: Article

References (20)

1. Bajorath, J.; Peltason, L.; Wawer, M.; Guha, R.; Lajiness, M. S.; Van Drie, J. H. Navigating Structure-Activity Landscapes Drug Discovery Today 2009, 14, 698-705
2. Peltason, L.; Bajorath, J. SAR Index: Quantifying the Nature of Structure-Activity Relationships J. Med. Chem. 2007, 50, 5571-5578 (Pubitemid 350106013)
3. Guha, R.; Van Drie, J. H. Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs J. Chem. Inf. Model 2008, 48, 646-658 (Pubitemid 351535432)
4. Leeson, P. D.; Davis, A. M.; Steele, J. Drug-like Properties: Guiding Principles for Design - or Chemical Prejudice Drug Discovery Today 2004, 1, 189-195 (Pubitemid 40197566)
5. Gillet, V. J.; Willet, P.; Bradshaw, J. Selecting Combinatorial Libraries to Optimize Diversity and Physical Properties J. Chem. Inf. Comput. Sci. 1999, 39, 167-177
6. Wright, T.; Gillet, V. J.; Green, D. S.; Pickett, S. D. Optimizing the Size and Configuration of Combinatorial Libraries J. Chem. Inf. Comput. Sci. 2003, 43, 381-390
7. Namasivayam, V.; Iyer, P.; Bajorath, J. Extraction of Discontinuous Structure-Activity Relationships from Compound Data Sets through Particle Swarm Optimization J. Chem. Inf. Model. 2011, 51, 1545-1551
8. Namasivayam, V.; Iyer, P.; Bajorath, J. Exploring SAR Continuity in the Vicinity of Activity Cliffs Chem. Biol. Drug Des. 2012, 79, 22-29
9. Kennedy, J.;; Eberhart, R. C. Particle Swarm Optimization. Proceedings IEEE International Conference Neural Networks IV (ICN95); 1995; pp 1942-1948.
10. Eberhart, R. C.; Shi, Y. Comparison between Genetic Algorithms and Particle Swarm Optimization Evol. Programming VII, Lect. Notes Comput. Sci. 1998, 1447, 611-616
11. Shi, Y.;; Eberhart, R. C. Parameter Selection in Particle Swarm Optimization. Proceedings of the Seventh Annual Conference on Evolutionary Programming; 1998; pp 591-600. (Pubitemid 128118969)
12. Kennedy, J.;; Eberhart, R. C. A Discrete Binary Version of the Particle Swarm Algorithm. Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics; 1997; pp 4104-4109.
13. Willett, P. Searching Techniques for Databases of Two- and Three-Dimensional Structures J. Med. Chem. 2005, 48, 4183-4199 (Pubitemid 40884919)
14. MACCS Structural Keys; Symyx Software: San Ramon, CA, 2005.
15. MOE (Molecular Operating Environment); Chemical Computing Group Inc.: Montreal, Quebec, Canada, 2011.
16. Lobell, M.; Hendrix, M.; Hinzen, B.; Keldnich, J.; Meier, H.; Schmeck, C.; Schohe-Loop, R.; Wunberg, T.; Hillisch, A. In silico ADMET Traffic Lights as Tool for the Prioritization of HTS Hits Chem. Med. Chem. 2006, 1, 1229-1236 (Pubitemid 44786929)
17. 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. 2012, 40, D1100-D1107
18. Reyes-Sierra, M.; Coello, C. A. C. Multi-Objective Particle Swarm Optimizers: A Survey of the State-of-the-Art Int. J. Comput. Intell. Res. 2006, 2, 287-309
19. Wickramasinghe, W.;; Li, X. Choosing Leaders for Multi-objective PSO Algorithms Using Differential Evolution. Proceedings of the Seventh International Conference on Simulated Evolution and Learning (SEAL′08); 2008; pp 249-258.
20. Clerc, M. Stagnation Analysis in Particle Swarm Optimization or What Happens When Nothing Happens; Technical Report CSM-460, Department of Computer Science, University of Essex, 2006; ISSN: 1744-8050.