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Improving Activity Prediction of Adenosine A2B Receptor Antagonists by Nonlinear Models

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9044))

Abstract

This study deals on estimation of ligand activity with its descriptors. So, to achieve this goal, two different approaches were implemented. In the first one, the intervals between samples were determined. But in the second method, the intervals were clustered with k-means method. Afterwards, best descriptors of each ligands were extracted with genetic algorithm. Then, observations were classified with One-Against-All method. Finally, the activity of each ligands were estimated by forty percent of samples. In the first method, AUC values were between fifty four to ninety seven percent. For second approaches, there were about ninety seven percent.

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References

  1. Bleicher, K.H., Böhm, H.-J., Müller, K., Alanine, A.I.: Hit and lead generation: beyond high-throughput screening. Nature Reviews Drug Discovery 2, 369–378 (2003)

    Article  Google Scholar 

  2. Bajorath, J.: Integration of virtual and high-throughput screening. Nature Reviews Drug Discovery 1, 882–894 (2002)

    Article  Google Scholar 

  3. Schneider, G., Fechner, U.: Computer-based de novo design of drug-like molecules. Nature Reviews Drug Discovery 4, 649–663 (2005)

    Article  Google Scholar 

  4. Hamza, A., Wei, N.-N., Zhan, C.-G.: Ligand-based virtual screening approach using a new scoring function. Journal of Chemical Information and Modeling 52, 963–974 (2012)

    Article  Google Scholar 

  5. Huggins, D.J., Venkitaraman, A.R., Spring, D.R.: Rational methods for the selection of diverse screening compounds. ACS Chemical Biology 6, 208–217 (2011)

    Article  Google Scholar 

  6. Butkiewicz, M., Lowe, E.W., Mueller, R., Mendenhall, J.L., Teixeira, P.L., Weaver, C.D., et al.: Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database. Molecules 18, 735–756 (2013)

    Article  Google Scholar 

  7. Ellingson, S.R., Baudry, J.: High-throughput virtual molecular docking with AutoDockCloud. Concurrency and Computation: Practice and Experience (2012)

    Google Scholar 

  8. Macarron, R., Banks, M.N., Bojanic, D., Burns, D.J., Cirovic, D.A., Garyantes, T., et al.: Impact of high-throughput screening in biomedical research. Nature Reviews Drug Discovery 10, 188–195 (2011)

    Article  Google Scholar 

  9. Ellingson, S.R., Baudry, J.: High-throughput virtual molecular docking: Hadoop implementation of AutoDock4 on a private cloud. In: Proceedings of the Second International Workshop on Emerging Computational Methods for the Life Sciences, pp. 33–38 (2011)

    Google Scholar 

  10. Collignon, B., Schulz, R., Smith, J.C., Baudry, J.: Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. Journal of computational chemistry 32, 1202–1209 (2011)

    Article  Google Scholar 

  11. Abdo, A., Salim, N.: Similarity-based virtual screening using bayesian inference network. Chemistry Central Journal 3, P44 (2009)

    Google Scholar 

  12. Jalali-Heravi, M., Mani-Varnosfaderani, A., Jahromi, P.E., Mahmoodi, M.M., Taherinia, D.: Classification of anti-HIV compounds using counterpropagation artificial neural networks and decision trees. SAR and QSAR in Environmental Research 22, 639–660 (2011)

    Article  Google Scholar 

  13. Theodoridis, S., Pikrakis, A., Koutroumbas, K., Cavouras, D.: Introduction to Pattern Recognition: A Matlab Approach: A Matlab Approach. Access Online via Elsevier (2010)

    Google Scholar 

  14. Jalali-Heravi, M., Mani-Varnosfaderani, A., Valadkhani, A.: Integrated One-Against-One Classifiers as Tools for Virtual Screening of Compound Databases: A Case Study with CNS Inhibitors. Molecular Informatics (2013)

    Google Scholar 

  15. Plewczynski, D., Spieser, S.A., Koch, U.: Assessing different classification methods for virtual screening. Journal of Chemical Information and Modeling 46, 1098–1106 (2006)

    Article  Google Scholar 

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Ghasemi, F. et al. (2015). Improving Activity Prediction of Adenosine A2B Receptor Antagonists by Nonlinear Models. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9044. Springer, Cham. https://doi.org/10.1007/978-3-319-16480-9_61

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  • DOI: https://doi.org/10.1007/978-3-319-16480-9_61

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-16479-3

  • Online ISBN: 978-3-319-16480-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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