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BioMed Research International
Volume 2014 (2014), Article ID 325959, 9 pages
An Infrastructure to Mine Molecular Descriptors for Ligand Selection on Virtual Screening
1Centro de Ciências Computacionais, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8 s/n, 96203-900 Rio Grande, RS, Brazil
2Departamento de Computação Aplicada, Universidade Federal de Santa Maria - USFM, Avenida Roraima 1000, 97105-900 Santa Maria, RS, Brazil
Received 21 December 2013; Accepted 14 February 2014; Published 9 April 2014
Academic Editor: Gabriela Mustata Wilson
Copyright © 2014 Vinicius Rosa Seus 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.
- X.-Y. Meng, H.-X. Zhang, M. Mezei, and M. Cui, “Molecular docking: a powerful approach for structure-based drug discovery,” Current Computer-Aided Drug Design, vol. 7, no. 2, pp. 146–157, 2011.
- E. Yuriev and P. A. Ramsland, “Latest developments in molecular docking: 2010–2011 in review,” Journal of Molecular Recognition, vol. 26, no. 5, pp. 215–239, 2013.
- T. Cheng, Q. Li, Z. Zhou, Y. Wang, and S. H. Bryant, “Structure-based virtual screening for drug discovery: a problem-centric review,” The AAPS Journal, vol. 14, no. 1, pp. 133–141, 2012.
- J. J. Irwin, T. Sterling, M. M. Mysinger, E. S. Bolstad, and R. G. Coleman, “Zinc: a free tool to discover chemistry for biology,” Journal of Chemical Information and Modeling, vol. 52, no. 7, pp. 1757–1768, 2012.
- E. E. Bolton, Y. Wang, P. A. Thiessen, and S. H. Bryant, “PubChem: integrated platform of small molecules and biological activities,” Annual Reports in Computational Chemistry, vol. 4, pp. 217–241, 2008.
- G. X. Perazzo, A. T. Winck, and K. S. Machado, “A data warehouse as an infrastructure to mine molecular descriptors for virtual screening,” in Proceedings of the 28th Annual ACM Symposium on Applied Computing (SAC '13), pp. 1335–1336, Coimbra, Portugal, 2013.
- G. M. Morris, R. Huey, W. Lindstrom et al., “AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility,” Journal of Computational Chemistry, vol. 30, no. 16, pp. 2785–2791, 2009.
- P. N. Tan, M. Steinbach, and V. Kumar, Introduction to Data Mining, Addison-Wesley Longman, Boston, Mass, USA, 1st edition, 2005.
- J. Han, M. Kamber, and J. Pei, Data Mining: Concepts and Techniques, Morgan Kaufmann, San Francisco, Calif, USA, 3rd edition, 2011.
- A. A. Freitas, D. C. Wieser, and R. Apweiler, “On the importance of comprehensible classification models for protein function prediction,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 1, pp. 172–182, 2010.
- I. H. Witten, E. Frank, and M. A. Hall, Data Mining: Practical Machine Learning Tools and Techniques, Morgan Kaufmann, Burlington, Mass, USA, 3rd edition, 2011.
- J. R. Quinlan, “Induction of decision trees,” Machine Learning, vol. 1, no. 1, pp. 81–106, 1986.
- I. D. Kuntz, “Structure-based strategies for drug design and discovery,” Science, vol. 257, no. 5073, pp. 1078–1082, 1992.
- C. P. Adams and V. V. Brantner, “Spending on new drug development,” Health Economics, vol. 19, no. 2, pp. 130–141, 2010.
- P. D. Lyne, “Structure-based virtual screening: an overview,” Drug Discovery Today, vol. 7, no. 20, pp. 1047–1055, 2002.
- H. Claußen, C. Buning, M. Rarey, and T. Lengauer, “FLEXE: efficient molecular docking considering protein structure variations,” Journal of Molecular Biology, vol. 308, no. 2, pp. 377–395, 2001.
- M. L. Verdonk, J. C. Cole, M. J. Hartshorn, C. W. Murray, and R. D. Taylor, “Improved protein-ligand docking using GOLD,” Proteins: Structure, Function and Genetics, vol. 52, no. 4, pp. 609–623, 2003.
- A. T. Winck, C. V. Quevedo, K. S. Machado, O. N. de Souza, and D. D. Ruiz, “A comparative analysis of public ligand databases based on molecular descriptors,” in Proceedings of the 7th Brazilian Symposium on Bioinformatics (BSB '12), vol. 7409, pp. 156–167, Campo Grande, Brazil, August 2012.
- K. P. Seiler, G. A. George, M. P. Happ et al., “ChemBank: a small-molecule screening and cheminformatics resource database,” Nucleic Acids Research, vol. 36, no. 1, pp. D351–D359, 2008.
- J. H. Chen, E. Linstead, S. J. Swamidass, D. Wang, and P. Baldi, “ChemDB update: full-text search and virtual chemical space,” Bioinformatics, vol. 23, no. 17, pp. 2348–2351, 2007.
- W.-D. Ihlenfeldt, J. H. Voigt, B. Bienfait, F. Oellien, and M. C. Nicklaus, “Enhanced CACTVS browser of the open NCI database,” Journal of Chemical Information and Computer Sciences, vol. 42, no. 1, pp. 46–57, 2002.
- C. P. Austin, L. S. Brady, T. R. Insel, and F. S. Collins, “Molecular biology: NIH molecular libraries initiative,” Science, vol. 306, no. 5699, pp. 1138–1139, 2004.
- E. E. Kim, C. T. Baker, M. D. Dwyer et al., “Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme,” Journal of the American Chemical Society, vol. 117, no. 3, pp. 1181–1182, 1995.
- A. Brik and C.-H. Wong, “HIV-1 protease: mechanism and drug discovery,” Organic & Biomolecular Chemistry, vol. 1, no. 1, pp. 5–14, 2003.
- W. Lindstrom, C. Weber, G. Morris, and R. Huey, Using AutoDock for Virtual Screening, Molecular Graphics Laboratory, the Scripps Research Institute, La Jolla, Calif, USA, 2008.
- F. H. Allen, “The cambridge structural database: a quarter of a million crystal structures and rising,” Acta Crystallographica B: Structural Science, vol. 58, no. 3, pp. 380–388, 2002.
- J. Masciocchi, G. Frau, M. Fanton, et al., “MMsINC: a large-scale chemoinformatics database,” Nucleic Acids Research, vol. 37, no. 1, pp. D284–D290, 2009.
- J. Portugal, “Evaluation of molecular descriptors for antitumor drugs with respect to noncovalent binding to DNA and antiproliferative activity,” BMC Pharmacology, vol. 9, article 11, 2009.
- R. Todeschini and V. Consonni, Handbook of Molecular Descriptors, John Wiley & Sons, Weinheim, Germany, 2000.
- R. Kimball and M. Ross, The Data Warehouse Toolkit: The Complete Guide to Dimensional Modeling, John Wiley & Sons, New York, NY, USA, 2nd edition, 2002.
- J. S. Cardoso and R. Sousa, “Measuring the performance of ordinal classification,” International Journal of Pattern Recognition and Artificial Intelligence, vol. 25, no. 8, pp. 1173–1195, 2011.
- C. A. Lipinski, “Drug-like properties and the causes of poor solubility and poor permeability,” Journal of Pharmacological and Toxicological Methods, vol. 44, no. 1, pp. 235–249, 2000.
- S. Murakami, R. Nakashima, E. Yamashita, and A. Yamaguchi, “Crystal structure of bacterial multidrug efflux transporter AcrB,” Nature, vol. 419, no. 6907, pp. 587–593, 2002.
- C. F. Higgins, “Multiple molecular mechanisms for multidrug resistance transporters,” Nature, vol. 446, no. 7137, pp. 749–757, 2007.