Enhancing molecular discovery using descriptor-free rearrangement clustering techniques for sparse data sets

AIChE Journal

Volumn 56, Issue 2, 2010, Pages 405-418

  DiMaggio Jr , Peter A ^a   McAllister, Scott R ^a   Floudas, Christodoulos A ^a   Feng, Xiao Jiang ^b   Li, Genyuan ^b   Rabinowitz, Joshua D ^b   Rabitz, Herschel A ^b  

^a Princeton University   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

Mathematical modeling; Optimization

Indexed keywords

CLUSTERING TECHNIQUES; COMPOUND LIBRARIES; COMPOUND SYNTHESIS; DESCRIPTORS; HEURISTIC APPROACH; INDEPENDENT ANALYSIS; ITERATIVE STRATEGY; ITERATIVE TECHNIQUE; LIBRARY COMPOUNDS; MATHEMATICAL MODELING; MILP MODEL; MINIMAL LIBRARIES; MIXED-INTEGER LINEAR PROGRAMMING; MOLECULAR SCAFFOLDS; OPTIMAL ENCODING; PERFORMANCE COMPARISON; SAMPLED DATA; SIMULATED EXPERIMENTS; SPARSE DATA SETS;

FUNCTIONAL GROUPS; INTEGER PROGRAMMING; LINEAR PROGRAMMING; LINEARIZATION; OPTIMIZATION; SYNTHESIS (CHEMICAL);

COMPLEXATION;

EID: 74349083201     PISSN: 00011541     EISSN: 15475905     Source Type: Journal    
DOI: 10.1002/aic.11986     Document Type: Article

References (27)

1. Ng R. Drugs-From Discovery to Approval. New Jersey: Wiley Liss, 2006.
2. Lutz M, Kenakin T. Quantitative molecular pharmacology and informatics in drug discovery. New Jersey: Wiley, 2001.
3. Bannwarth W, Hinzen B, Mannhold R, Kubinyi H, Folkers G. Combinatorial Chemistry: From Theory to Application (Methods and Principles in Medicinal Chemistry). New Jersey: Wiley-VCH, 2006.
4. Huser J, Mannhold R, Kubinyi H, Folkers G. High-Throughput Screening in Drug Discovery (Methods and Principles in Medicinal Chemistry). New Jersey: Wiley-VCH, 2006.
5. Hansch C, Leo A. Exploring QSAR-Fundamentals and Applications in Chemistry and Biology. Washington, DC: American Chemical Society, 1995.
6. Hansch C, Telzer BR, Zhang L. Comparative qsar in toxicology: examples from teratology and cancer chemotherapy of aniline mustards. Crit Rev Toxicol, 1995;25:67-89.
7. Perkins R, Fang H, Tong W, Welsh W. Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology. Environ Toxicol Chem. 2003;22:1666-1679.
8. Tong W, Welsh W, Shi L, Fang H, Perkins R. Structure-activity relationship approaches and applications. Environ Toxicol Chem, 2003;22:1680-1695.
9. Kahraman P, Turkay M. Classification of 1,4-dihydropyridine calcium channel antagonists using the hyperbox approach. Ind Eng Chem Res. 2007;46:4921-4929.
10. Armutlu P, Ozdemir ME, Uney-Yuksektepe F, Kavakli IH, Turkay M. Classification of drug molecules considering their ic50 values using mixed-integer linear programming based hyper-boxes method. BMC Bioinform. 2008;9:411-424.
11. Shenvi N, Geremia JM, Rabitz H. Substituent ordering and interpolation in molecular library optimization. J Phys Chem A. 2003;107:2066-2074.
12. Liang F, Feng X, Lowry M, Rabitz H. Maximal use of minimal libraries through the adaptive substituent reordering algorithm. J. Phys Chem B. 2005;109:5842-5854.
13. McCormick WT, Schweitzer PJ, White TW. Problem decomposition and data reorganization by a clustering technique. Oper Res. 1972;20:993-1009.
14. Lenstra JK. Clustering a data array and the traveling salesman problem. Oper Res. 1974;22:413-414.
15. Lenstra JK, Rinnooy Kan AHG. Some simple applications of the traveling salesman problem. Oper Res Q. 1975;26:717-733.
16. DiMaggio P, McAllister S, Floudas CA, Feng XJ, Rabinowitz J, Rabitz H. Biclustering via optimal reordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinform. 2008;9:458-473.
17. DiMaggio P, McAllister S, Floudas CA, Feng XJ, Rabinowitz J, Rabitz H. A network flow model for biclustering via optimal reordering of data matrices. J Glo Opt. In press.
18. Androulakis IP, Maranas CD, Floudas CA. Prediction of oligopeptide conformations via deterministic global optimization. J Glo Opt. 1997;11:1-34.
19. Klepeis JL, Floudas CA. Free energy calculations for peptides via deterministic global optimization. J Chem Phys. 1999;110:7491-7512.
20. Klepeis JL, Floudas CA, Morikis D, Lambris JD. Predicting peptide structures using NMR data and deterministic global optimization. J Comp Chem. 1999;20:1354-1370.
21. Klepeis JL, Floudas CA. Ab initio tertiary structure prediction of proteins. J Glo Opt. 2003;25:113-140.
22. Klepeis JL, Floudas CA. ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J. 2003;85:2119-2146.
23. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, Argyropoulos E, Spruce L, Lambris JD. Integrated computational and experimenal approach for lead optimization and design of compstatin variants with improved activity. J Am Chem Soc. 2003;125:8422-8423.
24. Fung HK, Floudas CA, Taylor MS, Zhang L, Morikis D. Towards full sequence de novo protein design with flexible templates for human beta-defensin-2. Biophys J. 2008;94:584-599.
25. Lin X, Floudas CA. Design, synthesis and scheduling of multipurpose batch plants via an effective continuous-time formulation. Comput Chem Eng. 2001;25:665-674.
26. Janak SL, Lin X, Floudas CA. Enhanced continuous-time unitspecific event based formulation for short-term scheduling of multipurpose batch processes: resource constraints and mixed storage policies. Ind Eng Chem Res. 2004;43:2516-2533.
27. CPLEX. ILOG CPLEX C++ API 11.1 Reference Manual. Gentilly, France: ILOG SA, 2008.