A novel and efficient ligand-based virtual screening approach using the HWZ scoring function and an enhanced shape-density model

References

• Akula, N., Zheng, H., Han, F. Q., & Wang, N. (2011). Discovery of novel SecA inhibitors of Candidatus Liberibacter asiaticus by structure based design. Bioorganic & Medicinal Chemistry Letters, 21, 4183–4188.
   PubMed Web of Science ®Google Scholar
• Belkin, N. J., Kantor, P., Fox, E. A., & Shaw, J. A. (1995). Combining the evidence of multiple query representations for information-retrieval. Information Processing & Management, 31, 431–448.
   Web of Science ®Google Scholar
• Bi, J., Yang, H., Yan, H., Song, R., & Fan, J. (2011). Knowledge-based virtual screening of HLA-A∗0201-restricted CD8(+) T-cell epitope peptides from herpes simplex virus genome. Journal of Theoretical Biology, 281, 133–139.
   PubMed Web of Science ®Google Scholar
• Bissantz, C., Folkers, G., & Rognan, D. (2000). Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. Journal of Medicinal Chemistry, 43, 4759–4767.
   PubMed Web of Science ®Google Scholar
• Bleicher, K. H., Green, L. G., Martin, R. E., & Rogers-Evans, M. (2004). Ligand identification for G-protein-coupled receptors: A lead generation perspective. Current Opinion in Chemical Biology, 8, 287–296.
   PubMed Web of Science ®Google Scholar
• Bostrom, J., Greenwood, J. R., & Gottfries, J. (2003). Assessing the performance of OMEGA with respect to retrieving bioactive conformations. Journal of Molecular Graphics & Modelling, 21, 449–462.
   PubMed Web of Science ®Google Scholar
• Chapman, P. B. (1967). Method of steepest descent. Canadian Mathematical Bulletin, 10: 133.
   Google Scholar
• Charifson, P. S., Corkery, J. J., Murcko, M. A., & Walters, W. P. (1999). Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. Journal of Medicinal Chemistry, 42, 5100–5109.
   PubMed Web of Science ®Google Scholar
• Coutsias, E. A., Seok, C., & Dill, K. A. (2004). Using quaternions to calculate RMSD. Journal of Computational Chemistry, 25, 1849–1857.
   PubMed Web of Science ®Google Scholar
• Coutsias, E. A., Seok, C., & Dill, K. A. (2005). Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. Journal of Computational Chemistry, 26, 1663–1665.
   PubMed Web of Science ®Google Scholar
• Cross, J. B., Thompson, D. C., Rai, B. K., Baber, J. C., Fan, K. Y., Hu, Y. B., & Humblet, C. (2009). Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy. Journal of Chemical Information and Modeling, 49, 1455–1474.
   PubMed Web of Science ®Google Scholar
• Diller, D. J., & Li, R. X. (2003). Kinases, homology models, and high throughput docking. Journal of Medicinal Chemistry, 46, 4638–4647.
   PubMed Web of Science ®Google Scholar
• Durrant, J. D., Friedman, A. J., & McCammon, J. A. (2011). CrystalDock: A novel approach to fragment-based drug design. Journal of Chemical Information and Modeling, 51, 2573–2580.
   PubMed Web of Science ®Google Scholar
• Englebienne, P., & Moitessier, N. (2009). Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? Journal of Chemical Information and Modeling, 49, 1568–1580.
   PubMed Web of Science ®Google Scholar
• Good, A. C., Krystek, S. R., & Mason, J. S. (2000). High-throughput and virtual screening: Core lead discovery technologies move towards integration. Drug Discovery Today, 5, S61–S69.
   PubMed Web of Science ®Google Scholar
• Grant, J. A., Gallardo, M. A., & Pickup, B. T. (1996). A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape. Journal of Computational Chemistry, 17, 1653–1666.
   Web of Science ®Google Scholar
• Grant, J. A., & Pickup, B. T. (1995). A GAUSSIAN description of molecular shape. Journal of Physical Chemistry, 99, 3503–3510.
   Web of Science ®Google Scholar
• Grant, J. A., & Pickup, B. T. (1996). A Gaussian description of molecular shape (vol 99, pg 3505, 1995). Journal of Physical Chemistry, 100, 2456–2456.
   Web of Science ®Google Scholar
• Hamza, A., Wei, N. N., & Zhan, C. G. (2012). Ligand-based virtual screening approach using a new scoring function. Journal of Chemical Information and Modeling, 52, 963–974.
   PubMed Web of Science ®Google Scholar
• Hamza, A., Zhao, X., Tong, M., Tai, H. H., & Zhan, C. G. (2011). Novel human mPGES-1 inhibitors identified through structure-based virtual screening. Bioorganic & Medicinal Chemistry, 19, 6077–6086.
   Google Scholar
• Hecker, E. A., Duraiswami, C., Andrea, T. A., & Diller, D. J. (2002). Use of catalyst pharmacophore models for screening of large combinatorial libraries. Journal of Chemical Information and Computer Sciences, 42, 1204–1211.
   PubMedGoogle Scholar
• Hert, J., Willett, P., & Wilton, D. J. (2004a). Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. Journal of Chemical Information and Computer Sciences, 44, 1177–1185.
   PubMedGoogle Scholar
• Hert, J., Willett, P., Wilton, D. J., Acklin, P., Azzaoui, K., Jacoby, E., & Schuffenhauer, A. (2004b). Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Organic & Biomolecular Chemistry, 2, 3256–3266.
   PubMed Web of Science ®Google Scholar
• Hert, J., Willett, P., Wilton, D. J., Acklin, P., Azzaoui, K., Jacoby, E., & Schuffenhauer, A. (2006). 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, 46, 462–470.
   PubMed Web of Science ®Google Scholar
• Hodgkin, E. E., & Richards, W. G. (1987). Molecular similarity based on electrostatic potential and electric-field. International Journal of Quantum Chemistry, 14, 105–110.
   Google Scholar
• Hsu, D. F., & Taksa, I. (2005). Comparing rank and score combination methods for data fusion in information retrieval. Information Retrieval, 8, 449–480.
   Google Scholar
• Huang, N., Shoichet, B. K., & Irwin, J. J. (2006). Benchmarking sets for molecular docking. Journal of Medicinal Chemistry, 49, 6789–6801.
   PubMed Web of Science ®Google Scholar
• Jacobsson, M., Liden, P., Stjernschantz, E., Bostrom, H., & Norinder, U. (2003). Improving structure-based virtual screening by multivariate analysis of scoring data. Journal of Medicinal Chemistry, 46, 5781–5789.
   PubMed Web of Science ®Google Scholar
• Jahn, A., Hinselmann, G., Nikolas Fechner, N., & Zell, A. (2009). Optimal assignment methods for ligand-based virtual screening. Journal of Cheminformatics, 1, 1–23.
   PubMed Web of Science ®Google Scholar
• Jain, A. N. (2004). Ligand-based structural hypotheses for virtual screening. Journal of Medicinal Chemistry, 47, 947–961.
   PubMed Web of Science ®Google Scholar
• John, S., Thangapandian, S., Sakkiah, S., & Lee, K. W. (2011). Discovery of potential pancreatic cholesterol esterase inhibitors using pharmacophore modelling, virtual screening, and optimization studies. Journal of Enzyme Inhibition and Medicinal Chemistry, 26, 535–545.
   PubMed Web of Science ®Google Scholar
• Karney, C. F. F. (2007). Quaternions in molecular modeling. Journal of Molecular Graphics & Modelling, 25, 595–604.
   PubMed Web of Science ®Google Scholar
• Kinnings, S. L., & Jackson, R. M. (2009). LigMatch: A multiple structure-based ligand matching method for 3d virtual screening. Journal of Chemical Information and Modeling, 49, 2056–2066.
   PubMed Web of Science ®Google Scholar
• Kirchmair, J., Distinto, S., Markt, P., Schuster, D., Spitzer, G. M., Liedl, K. R., & Wolber, G. (2009). How to optimize shape-based virtual screening: Choosing the right query and including chemical information. Journal of Chemical Information and Modeling, 49, 678–692.
   PubMed Web of Science ®Google Scholar
• Liu, X. F., Jiang, H. L., & Li, H. L. (2011). SHAFTS: A hybrid approach for 3d molecular similarity calculation. 1. Method and assessment of virtual screening. Journal of Chemical Information and Modeling, 51, 2372–2385.
   PubMed Web of Science ®Google Scholar
• Mezey, P. G. (1993). Topological shape-analysis of chain molecules: An application of the GSTE principle. Journal of Mathematical Chemistry, 12, 365–373.
   Web of Science ®Google Scholar
• Ng, K. B., & Kantor, P. B. (2000). Predicting the effectiveness of naive data fusion on the basis of system characteristics. Journal of the American Society for Information Science, 51, 1177–1189.
   Google Scholar
• Nicholls, A. (2008). What do we know and when do we know it? Journal of Computer-Aided Molecular Design, 22, 239–255.
   PubMed Web of Science ®Google Scholar
• OMEGA-2.2 (2007). Open eye scientific software. www.eyesopen.com
   Google Scholar
• Patel, Y., Gillet, V. J., Bravi, G., & Leach, A. R. (2002). A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP. Journal of Computer-Aided Molecular Design, 16, 653–681.
   PubMed Web of Science ®Google Scholar
• Presnell, S. R., Patil, G. S., Mura, C., Jude, K. M., Conley, J. M., Bertrand, J. A., & Williams, L. D. (1998). Oxyanion-mediated inhibition of serine proteases. Biochemistry, 37, 17068–17081.
   PubMed Web of Science ®Google Scholar
• Randic, M. (1975). Characterization of molecular branching. Journal of the American Chemical Society, 97, 6609–6615.
   Web of Science ®Google Scholar
• Randic, M. (1984). Nonempirical approach to structure activity studies. International Journal of Quantum Chemistry, 26, 137–153.
   Google Scholar
• Rogers, D. J., & Tanimoto, T. T. (1960). A computer program for classifying plants. American Association for the Advancement of Science, 132, 1115–1118.
   Google Scholar
• Rouvray, D. H. (1986). Predicting chemistry from topology. Scientific American, 255, 40–47.
   Google Scholar
• Sastry, G. M., Dixon, S. L., & Sherman, W. (2011). Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring. Journal of Chemical Information and Modeling, 51, 2455–2466.
   PubMed Web of Science ®Google Scholar
• Schneider, G., & Bohm, H. J. (2002). Virtual screening and fast automated docking methods. Drug Discovery Today, 7, 64–70.
   PubMed Web of Science ®Google Scholar
• Steinmet, H. L. (1966). Using method of steepest descent. Industrial and Engineering Chemistry, 58, 33–39.
   Google Scholar
• Triballeau, N., Acher, F., Brabet, I., Pin, J. P., & Bertrand, H. O. (2005). Virtual screening workflow development guided by the “receiver operating characteristic” curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. Journal of Medicinal Chemistry, 48, 2534–2547.
   PubMed Web of Science ®Google Scholar
• Truchon, J. F., & Bayly, C. I. (2007). Evaluating virtual screening methods: Good and bad metrics for the “early recognition” problem. Journal of Chemical Information and Modeling, 47, 488–508.
   PubMed Web of Science ®Google Scholar
• Vainio, M. J., Puranen, J. S., & Johnson, M. S. (2009). ShaEP: Molecular overlay based on shape and electrostatic potential. Journal of Chemical Information and Modeling, 49, 492–502.
   PubMed Web of Science ®Google Scholar
• Vand, V. (1951). A simplified method of steepest descents. Acta Crystallographica, 4, 285–286.
   Google Scholar
• Vasilescu, D. & Viani, R. (1987). Molecular similarity in aminothiol radioprotectors: A randic graph approach. International Journal of Quantum Chemistry, 14, 149–165.
   Google Scholar
• Venkatraman, V., Perez-Nueno, V. I., Mavridis, L., & Ritchie, D. W. (2010). Comprehensive comparison of ligand-based virtual screening tools against the dud data set reveals limitations of current 3D methods. Journal of Chemical Information and Modeling, 50, 2079–2093.
   PubMed Web of Science ®Google Scholar
• Walker, P. D., Arteca, G. A., & Mezey, P. G. (1991). A complete shape characterization for molecular charge-densities represented by Gaussian-type functions. Journal of Computational Chemistry, 12, 220–230.
   Web of Science ®Google Scholar
• Wang, R. X., & Wang, S. M. (2001). How does consensus scoring work for virtual library screening? An idealized computer experiment. Journal of Chemical Information and Computer Sciences, 41, 1422–1426.
   PubMedGoogle Scholar
• Zhang, Q., & Muegge, I. (2006). Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring. Journal of Medicinal Chemistry, 49, 1536–1548.
   PubMed Web of Science ®Google Scholar