Network and Pathway Analysis of Compound–Protein Interactions

Methods in Molecular Biology

Volumn 575, Issue , 2009, Pages 225-247

  Brennan, Richard J ^a   Nikolskya, Tatiana ^a   Bureeva, Svetlana ^a  

^a GeneGo   (United States)

Author keywords

Functional analysis; Network reconstruction; Pathway analysis; Structural similarity search; Target prediction

Indexed keywords

PROTEIN;

ARTICLE; CHEMISTRY; DRUG DEVELOPMENT; FACTUAL DATABASE; METABOLOMICS; METHODOLOGY; MOLECULAR BIOLOGY; PROTEIN ANALYSIS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICS; SYSTEMS BIOLOGY;

DATABASES, FACTUAL; DRUG DISCOVERY; METABOLOMICS; MOLECULAR BIOLOGY; PROTEIN INTERACTION MAPPING; PROTEINS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SYSTEMS BIOLOGY;

MLCS; MLOWN;

EID: 75549089718     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-274-2_10     Document Type: Chapter

References (20)

1. Ekins, S., Bugrim, A., Nikolsky, Y., and Nikolskya, T. (2005) Systems biology: applications in drug discovery. In: Gad, S. C. (ed.) Drug Discovery Handbook. Wiley-Interscience, Hoboken, pp. 123–183.
2. Nikolsky, Y., Nikolskaya, T., and Bugrim, A. (2005) Biological networks and analysis of experimental data in drug discovery. Drug Discov. Today 10, 653–662.
3. Richard, A. M., Yang, C., and Judson, R. S. (2008) Toxicity data informatics: support-ing a new paradigm for toxicity prediction. Toxicol. Mech. Methods 18, 103–118.
4. Bender, A., Young, D. W., Jenkins, J. L., et al. (2007) Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint. Comb. Chem. High Throughput Screen. 10, 719– 731.
5. Young, D. W., Bender, A., Hoyt, J., et al. (2008) Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat. Chem. Biol. 4, 59–68.
6. Ekins, S., Andreyev, S., Ryabov, A., et al. (2006) A combined approach to drug metabolism and toxicity assessment. Drug Metab. Dispos. 34, 495–503.
7. Ekins, S., Bugrim, A., Brovold, L., et al. (2006) Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms. Xenobiotica 36, 877–901.
8. Herrmann, M. L., Schleyerbach, R., and Kirschbaum, B. J. (2000) Leflunomide: an immunomodulatory drug for the treatment of rheumatoid arthritis and other autoim-mune diseases. Immunopharmacology 47, 273–289.
9. Etienne, F., Resnick, L., Sagher, D., Brot, N., and Weissbach, H. (2003) Reduction of sulindac to its active metabolite, sulindac sulfide: assay and role of the methionine sul-foxide reductase system. Biochem. Biophys. Res. Commun. 312, 1005–1010.
10. Murrell, G. A. and Rapeport, W. G. (1986) Clinical pharmacokinetics of allopurinol. Clin. Pharmacokinet. 11, 343–353.
11. Smith, S. J. (1994) Cardiovascular toxicity of antihistamines. Otolaryngol. Head Neck Surg. 111, 348–354.
12. Humphreys, W. G. (2007) Drug metabolism research as an integral part of the drug discovery process. In: Zhang, D., Zhu, M., and Humphreys, W. G. (eds.) Drug Metabolism in Drug Design and Development. Wiley-Interscience, Hoboken, pp. 239–260.
13. Rusinko, A. III, Farmen, M. W., Lambert, C. G., Brown, P. L., and Young, S. S. (1999) Analysis of a large structure/bio-logical activity data set using recursive par-titioning. J. Chem. Inf. Comput. Sci. 39, 1017–1026.
14. Blower, P. E. and Cross, K. P. (2006) Deci-sion tree methods in pharmaceutical research. Curr. Top. Med. Chem. 6, 31–39.
15. Willett, P., Winterman, V., and Bawden, D. (1986) Implementation of nearest-neighbor searching in an online chemical structure search system. J. Chem. Inf. Comput. Sci. 26, 36–41.
16. Matter, H. (1997) Selecting optimally diverse compounds from structure data-bases: a validation study of two-dimensional and three-dimensional molecular descrip-tors. J. Med. Chem. 40, 1219–1229.
17. Khatri, P. and Draghici, S. (2005) Ontologi-cal analysis of gene expression data: current tools, limitations, and open problems. Bio-informatics 21, 3587–3595.
18. Ekins, S., Nikolsky, Y., Bugrim, A., Kirillov, E., and Nikolskaya, T. (2007) Pathway map-ping tools for analysis of high content data. Methods Mol. Biol. 356, 319–350.
19. Shipitsin, M., Campbell, L. L., Argani, P., et al. (2007) Molecular definition of breast tumor heterogeneity. Cancer Cell 11, 259– 273.
20. Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J. (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 46, 3–26.