Reagent Selector: Using Synthon Analysis to visualize reagent properties and assist in combinatorial library design

Journal of Chemical Information and Modeling

Volumn 45, Issue 5, 2005, Pages 1439-1446

  Mosley, Ralph T ^a   Culberson, J Christopher ^a   Kraker, Bryan ^a   Feuston, Bradley P ^a   Sheridan, Robert P ^a   Conway, John F ^a   Forbes, Joseph K ^a   Chakravorty, Subhas J ^a   Kearsley, Simon K ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMBINATORIAL MATHEMATICS; GRAPH THEORY; TOPOLOGY; VISUALIZATION;

PHYSICOCHEMICAL PROPERTIES; REAGENT SELECTOR; REFINES; SYNTHON;

AMINES;

DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; G PROTEIN COUPLED RECEPTOR;

ARTICLE; COMBINATORIAL CHEMISTRY; METABOLISM;

COMBINATORIAL CHEMISTRY TECHNIQUES; INDICATORS AND REAGENTS; RECEPTORS, G-PROTEIN-COUPLED;

EID: 26944499805     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050090x     Document Type: Article

References (17)

1. Blaney, J. M.; Martin, E. J. Computational approaches for combinatorial library design and molecular diversity analysis. Curr. Opin. Chem. Biol. 1997, 1, 54-59.
2. Brown, R. D.; Hassan, M.; Waldman, M. Combinatorial library design for diversity, cost efficiency, and drug-like character. J. Mol. Graph. Model. 2000, 18, 427-437.
3. Polinsky, A.; Feinstein, R. D.; Shi, S.; Kuki, A. LiBrain: software for automated design of exploratory and targeted combinatorial libraries of special interest. In Molecular Diversity and Combinatorial Chemistry; Chaiken, I. M., Janda, K. D., Eds.; American Chemical Society: Washington, DC, 1996; pp 219-232.
4. For example, MDL's Reagent Selector, MDL Information Systems, Inc., San Leandro, CA.
5. Jamois, E. A.; Hassan, M.; Waldman, M. Evaluation of Reagent-Based and Product-Based Strategies in the Design of Combinatorial Library Subsets. J. Chem. Inf. Comput. Sci. 2000, 40, 63-70.
6. Martin, E. J.; Blaney, J. M.; Siani, M. A.; Spellmeyer, D. C.; Wong, A. K.; Moos, W. H. Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery. J. Med. Chem. 1995, 38, 1431-1436.
7. Brown, R. D.; Martin, Y. C. Use of Structure-Activity Data to Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
8. Feuston, B. P.; Chakravorty, S. J.; Conway, J. F.; Culberson, J. C.; Forbes, J.; Kraker, B.; Lennon, P. A.; Lindsley, C.; McGaughey, G. B.; Mosley, R.; Sheridan, R. P.; Valenciano, M.; Kearsley, S. K. Web enabling technology for the design, enumeration, optimization and tracking of compound libraries. Curr. Topics Med. Chem. 2005, accepted for publication.
9. Kraker, B.; Chakravorty, S. J.; Mosley, R. T.; Culberson, J. C.; Feuston, B. P.; Sheridan, R. P.; Conway, J. F.; Forbes, J. K.; Kearsley, S. K. Virtual Library Tool Kit: Comparison of functional group queries with Daylight and ISIS software, manuscript in preparation.
10. Bush, B. L.; Sheridan, R. P. PATTY: A programmable atom type and language for automatic classification of atoms in molecular databases. J. Chem. Inf. Comput. Sci. 1993, 33, 756-762.
11. Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. FLOG: a system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 153-174.
12. Butina, D. Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way to Cluster Small and Large Data Sets. J. Chem. Inf. Comput. Sci. 1999, 39, 747-750.
13. Holliday, J. D.; Jelfs, S. P.; Willett, P. Calculation of Intersubstituent Similarity Using R-Group Descriptors. J. Chem. Inf. Comput. Sci. 2003, 43, 406-411.
14. Bemis, G. W.; Murcko, M. A. Properties of Known Drugs. 2. Side Chains. J. Med. Chem. 1999, 42, 5095-5099.
15. Gasteiger, J.; Rudolf, C.; Sadowski, J. Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comput. Methodol. 1990, 3, 537-547.
16. Rohrer, S. P.; Birzin, E. T.; Mosley, R. T.; Berk, S. C.; Hutchins, S. M.; Shen, D.-M.; Xiong, Y.; Hayes, E. C.; Parmar, R. M.; Foor, F.; Mitra, S. W.; Degrado, S. J.; Shu, M.; Klopp, J. M.; Cai, S.-J.; Blake, A.; Chan, W. W. S.; Pasternak, A.; Yang, L.; Patchett, A. A.; Smith, R. G.; Chapman, K. T.; Schaeffer, J. M. Rapid identification of subtype-selective agonists of the somatostatin receptor through combinatorial chemistry. Science 1998, 282, 737-740.
17. Berk, S. C.; Rohrer, S. P.; Degrado, S. J.; Birzin, E. T.; Mosley, R. T.; Hutchins, S. M.; Pasternak, A.; Schaeffer, J. M.; Underwood, D. J.; Chapman, K. T. A Combinatorial Approach toward the Discovery of Non-Peptide, Subtype-Selective Somatostatin Receptor Ligands, J. Comb. Chem. 1999, 1, 388-396.