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The Scientific World Journal
Volume 2012 (2012), Article ID 410914, 7 pages
Ligand-Based Virtual Screening Using Bayesian Inference Network and Reweighted Fragments
1Faculty of Computer Science and Information Systems, Universiti Tecknologi Malaysia, 81310 Skudai, Malaysia
2Faculty of Engineering, Karary University, Khartoum 12304, Sudan
3Department of Computer Science, Hodeidah University, Hodeidah, Yemen
Received 28 October 2011; Accepted 11 December 2011
Academic Editors: M. A. Fischl and G. D. Morse
Copyright © 2012 Ali Ahmed et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- M. A. Johnson and G. M. Maggiora, Concepts and Application of Molecular Similarity, John Wiley & Sons, New York, NY, USA, 1990.
- P. Willett, J. M. Barnard, and G. M. Downs, “Chemical similarity searching,” Journal of Chemical Information and Computer Sciences, vol. 38, no. 6, pp. 983–996, 1998.
- W. P. Walters, M. T. Stahl, and M. A. Murcko, “Virtual screening—an overview,” Drug Discovery Today, vol. 3, no. 4, pp. 160–178, 1998.
- B. Waszkowycz, T. D. J. Perkins, R. A. Sykes, and J. Li, “Large-scale virtual screening for discovering leads in the postgenomic era,” IBM Systems Journal, vol. 40, no. 2, pp. 360–378, 2001.
- M. A. Miller, “Chemical database techniques in drug discovery,” Nature Reviews Drug Discovery, vol. 1, no. 3, pp. 220–227, 2002.
- H. Eckert and J. Bajorath, “Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches,” Drug Discovery Today, vol. 12, no. 5-6, pp. 225–233, 2007.
- R. P. Sheridan, “Chemical similarity searches: when is complexity justified?” Expert Opinion on Drug Discovery, vol. 2, no. 4, pp. 423–430, 2007.
- H. Geppert, M. Vogt, and J. Bajorath, “Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation,” Journal of Chemical Information and Modeling, vol. 50, no. 2, pp. 205–216, 2010.
- R. P. Sheridan and S. K. Kearsley, “Why do we need so many chemical similarity search methods?” Drug Discovery Today, vol. 7, no. 17, pp. 903–911, 2002.
- N. Nikolova and J. Jaworska, “Approaches to measure chemical similarity—a Review,” QSAR & Combinatorial Science, vol. 22, no. 9-10, pp. 1006–1026, 2003.
- A. Bender and R. C. Glen, “Molecular similarity: a key technique in molecular informatics,” Organic and Biomolecular Chemistry, vol. 2, no. 22, pp. 3204–3218, 2004.
- A. G. Maldonado, J. P. Doucet, M. Petitjean, and B. T. Fan, “Molecular similarity and diversity in chemoinformatics: from theory to applications,” Molecular Diversity, vol. 10, no. 1, pp. 39–79, 2006.
- A. R. Leach and V. J. Gillet, An Introduction to Chemoinformatics, Springer, 2007.
- P. Willett, “Enhancing the effectiveness of ligand-based virtual screening using data fusion,” QSAR & Combinatorial Science, vol. 25, no. 12, pp. 1143–1152, 2006.
- L. Hodes, “Clustering a large number of compounds. 1. Establishing the method on an initial sample,” Journal of Chemical Information and Computer Sciences, vol. 29, pp. 66–71, 1989.
- P. Willett and V. Winterman, “A comparison of some measures for the determination of inter-molecular structural similarity measures of inter-molecular structural similarity,” Quantitative Structure-Activity Relationships, vol. 5, no. 1, pp. 18–25, 1986.
- P. A. Bath, C. A. Morris, and P. Willett, “Effect of standardization on fragment‐based measures of structural similarity,” Journal of chemometrics, vol. 7, pp. 543–550, 1993.
- J. D. Holliday, C. Y. Hu, and P. Willett, “Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings,” Combinatorial Chemistry & High Throughput Screening, vol. 5, no. 2, pp. 155–166, 2002.
- H. Turtle and W. B. Croft, “Evaluation of an inference network-based retrieval model,” ACM Transactions on Information Systems, vol. 9, pp. 187–222, 1991.
- D. Haines and W. B. Croft, “Relevance feedback and inference networks,” in Proceedings of the 16th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '93), pp. 2–11, July 1993.
- L. M. De Campos, J. M. Fernández-Luna, and J. F. Huete, “Implementing relevance feedback in the Bayesian network retrieval model,” Journal of the American Society for Information Science & Technology, vol. 54, no. 4, pp. 302–313, 2003.
- J. Xin and J. S. Jin, “Relevance feedback for content-based image retrieval using Bayesian network,” in Proceedings of the Pan-Sydney Area Workshop on Visual Information Processing (VIP '05), pp. 91–94, 2004.
- A. Abdo, N. Salim, and A. Ahmed, “Implementing relevance feedback in ligand-based virtual screening using bayesian inference network,” Journal of Biomolecular Screening, vol. 16, no. 9, pp. 1081–1088, 2011.
- A. Abdo and N. Salim, “New fragment weighting scheme for the Bayesian inference network in ligand-based virtual screening,” Journal of Chemical Information and Modeling, vol. 51, no. 1, pp. 25–32, 2011.
- D. Ellis, J. F. Hines, and P. Willett, “Measuring the degree of similarity between objects in text retrieval systems,” Perspectives in Information Management, vol. 3, pp. 128–149, 1993.
- A. Abdo and N. Salim, “Similarity-based virtual screening with a bayesian inference network,” ChemMedChem, vol. 4, no. 2, pp. 210–218, 2009.
- B. Chen, C. Mueller, and P. Willett, “Evaluation of a Bayesian inference network for ligand-based virtual screening,” Journal of Cheminformatics, vol. 1, article 5, 2009.
- Pipeline Pilot, Accelrys Software, San Diego, Calif, USA, 2008.
- J. Hert, P. Willett, D. J. Wilton et al., “New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching,” Journal of Chemical Information and Modeling, vol. 46, no. 2, pp. 462–470, 2006.
- S. Siegel and N. J. Castellan, Nonparametric Statistics for the Behavioral Sciences, McGraw-Hill, 1988.