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Volumn 48, Issue 1, 2008, Pages 166-178

Naïve Bayes classification using 2D pharmacophore feature triplet vectors

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN NETWORKS; CLASSIFICATION (OF INFORMATION); DATABASE SYSTEMS; DRUG PRODUCTS; FEATURE EXTRACTION; VECTORS;

EID: 39449088858     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci7003253     Document Type: Article
Times cited : (64)

References (47)
  • 1
    • 21244468757 scopus 로고    scopus 로고
    • Searching techniques for databases of two- and three-dimensional chemical structures
    • Willett, P. Searching techniques for databases of two- and three-dimensional chemical structures. J. Med. Chem. 2005, 48, 4183-4199.
    • (2005) J. Med. Chem , vol.48 , pp. 4183-4199
    • Willett, P.1
  • 2
    • 10344230435 scopus 로고    scopus 로고
    • Molecular similarity: A key technique in molecular informatics
    • Bender, A.; Glen, R. C. Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem 2004, 2, 3204-3218.
    • (2004) Org. Biomol. Chem , vol.2 , pp. 3204-3218
    • Bender, A.1    Glen, R.C.2
  • 3
    • 33751246188 scopus 로고    scopus 로고
    • Similarity-based virtual screening using 2D fingerprints
    • Willett, P. Similarity-based virtual screening using 2D fingerprints. Drug Discovery Today 2006, 11, 1046-1053.
    • (2006) Drug Discovery Today , vol.11 , pp. 1046-1053
    • Willett, P.1
  • 4
    • 5544290537 scopus 로고    scopus 로고
    • Similarity searching of chemical databases using atom environment descriptors (MOL-PRINT 2D): Evaluation of performance
    • Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity searching of chemical databases using atom environment descriptors (MOL-PRINT 2D): evaluation of performance. J. Chem. Inf. Comput. Sci. 2004, 44, 1708-1718.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 1708-1718
    • Bender, A.1    Mussa, H.Y.2    Glen, R.C.3    Reiling, S.4
  • 5
    • 10244222365 scopus 로고    scopus 로고
    • Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
    • Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org. Biomol. Chem 2004, 2, 3256-3266.
    • (2004) Org. Biomol. Chem , vol.2 , pp. 3256-3266
    • Hert, J.1    Willett, P.2    Wilton, D.J.3    Acklin, P.4    Azzaoui, K.5    Jacoby, E.6    Schuffenhauer, A.7
  • 7
    • 18344367660 scopus 로고    scopus 로고
    • LINGO, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities
    • Vidal, D.; Thormann, M.; Pons, M. LINGO, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities. J. Chem. Inf. Model. 2005, 45, 386-393.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 386-393
    • Vidal, D.1    Thormann, M.2    Pons, M.3
  • 9
    • 14944348527 scopus 로고    scopus 로고
    • A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
    • Rush, T. S., III; Grant, J. A.; Mosyak, L.; Nicholls, A. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J. Med. Chem. 2005, 48, 1489-1495.
    • (2005) J. Med. Chem , vol.48 , pp. 1489-1495
    • Rush III, T.S.1    Grant, J.A.2    Mosyak, L.3    Nicholls, A.4
  • 10
    • 33646251359 scopus 로고    scopus 로고
    • Similarity searching in databases of flexible 3D structures using autocorrelation vectors derived from smoothed bounded distance matrices
    • Rhodes, N.; Clark, D. E.; Willett, P. Similarity searching in databases of flexible 3D structures using autocorrelation vectors derived from smoothed bounded distance matrices. J. Chem. Inf. Model. 2006, 46, 615-619.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 615-619
    • Rhodes, N.1    Clark, D.E.2    Willett, P.3
  • 11
    • 34547260921 scopus 로고    scopus 로고
    • Ultrafast shape recognition to search compound databases for similar molecular shapes
    • Ballester, P. J.; Richards, W. G. Ultrafast shape recognition to search compound databases for similar molecular shapes. J. Comput. Chem. 2007, 28, 1711-1723.
    • (2007) J. Comput. Chem , vol.28 , pp. 1711-1723
    • Ballester, P.J.1    Richards, W.G.2
  • 13
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput.-Aided Mol. Des. 2001, 15, 411-428.
    • (2001) J. Comput.-Aided Mol. Des , vol.15 , pp. 411-428
    • Ewing, T.J.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 15
    • 0029705324 scopus 로고    scopus 로고
    • Automated docking of flexible ligands: Applications of AutoDock
    • Goodsell, D. S.; Morris, G. M.; Olson, A. J. Automated docking of flexible ligands: applications of AutoDock. J. Mol. Recognit. 1996, 9, 1-5.
    • (1996) J. Mol. Recognit , vol.9 , pp. 1-5
    • Goodsell, D.S.1    Morris, G.M.2    Olson, A.J.3
  • 16
    • 1642310340 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    • Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47, 1750-1759.
    • (2004) J. Med. Chem , vol.47 , pp. 1750-1759
    • Halgren, T.A.1    Murphy, R.B.2    Friesner, R.A.3    Beard, H.S.4    Frye, L.L.5    Pollard, W.T.6    Banks, J.L.7
  • 17
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 19
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
    • Morris, G. M.; Goodsell, D. S.; Huey, R.; Olson, A. J. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J. Comput.-Aided Mol. Des. 1996, 10, 293-304.
    • (1996) J. Comput.-Aided Mol. Des , vol.10 , pp. 293-304
    • Morris, G.M.1    Goodsell, D.S.2    Huey, R.3    Olson, A.J.4
  • 20
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
    • (1996) J. Mol. Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 23
    • 33846212271 scopus 로고    scopus 로고
    • Comparison of shape-matching and docking as virtual screening tools
    • Hawkins, P. C.; Skillman, A. G.; Nicholls, A. Comparison of shape-matching and docking as virtual screening tools. J. Med. Chem. 2007, 50, 74-82.
    • (2007) J. Med. Chem , vol.50 , pp. 74-82
    • Hawkins, P.C.1    Skillman, A.G.2    Nicholls, A.3
  • 24
    • 77956734967 scopus 로고    scopus 로고
    • Machine Learning In Computational Chemistry
    • Goldman, B.; Walters, P. Machine Learning In Computational Chemistry. Annu. Rep. Comput. Chem. 2006, 2, 127-140.
    • (2006) Annu. Rep. Comput. Chem , vol.2 , pp. 127-140
    • Goldman, B.1    Walters, P.2
  • 27
    • 0345548661 scopus 로고    scopus 로고
    • Comparison of support vector machine and artificial neural network systems for drug/nondrug classification
    • Byvatov, E.; Fechner, U.; Sadowski, J.; Schneider, G. Comparison of support vector machine and artificial neural network systems for drug/nondrug classification. J. Chem. Inf. Comput. Sci. 2003, 43, 1882-1889.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 1882-1889
    • Byvatov, E.1    Fechner, U.2    Sadowski, J.3    Schneider, G.4
  • 28
    • 2942702317 scopus 로고    scopus 로고
    • SVM-based feature selection for characterization of focused compound collections
    • Byvatov, E.; Schneider, G. SVM-based feature selection for characterization of focused compound collections. J. Chem. Inf. Comput. Sci. 2004, 44, 993-999.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 993-999
    • Byvatov, E.1    Schneider, G.2
  • 29
    • 0345040882 scopus 로고    scopus 로고
    • Support vector machine applications in bioinformatics
    • Byvatov, E.; Schneider, G. Support vector machine applications in bioinformatics. Appl. Bioinformatics 2003, 2, 67-77.
    • (2003) Appl. Bioinformatics , vol.2 , pp. 67-77
    • Byvatov, E.1    Schneider, G.2
  • 30
    • 0345548657 scopus 로고    scopus 로고
    • Svetnik, V.; Liaw, A.; Tong, C.; Culberson, J. C.; Sheridan, R. P.; Feuston, B. P. Random forest: a classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Comput. Sci. 2003, 43, 1947-1958.
    • Svetnik, V.; Liaw, A.; Tong, C.; Culberson, J. C.; Sheridan, R. P.; Feuston, B. P. Random forest: a classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Comput. Sci. 2003, 43, 1947-1958.
  • 31
    • 23844450432 scopus 로고    scopus 로고
    • Genetic programming for the induction of decision trees to model ecotoxicity data
    • Buontempo, F. V.; Wang, X. Z.; Mwense, M.; Horan, N.; Young, A.; Osborn, D. Genetic programming for the induction of decision trees to model ecotoxicity data. J. Chem. Inf. Model. 2005, 45, 904-912.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 904-912
    • Buontempo, F.V.1    Wang, X.Z.2    Mwense, M.3    Horan, N.4    Young, A.5    Osborn, D.6
  • 32
    • 26944502743 scopus 로고    scopus 로고
    • Effect of selection of molecular descriptors on the prediction of blood-brain barrier penetrating and nonpenetrating agents by statistical learning methods
    • Li, H.; Yap, C. W.; Ung, C. Y.; Xue, Y.; Cao, Z. W.; Chen, Y. Z. Effect of selection of molecular descriptors on the prediction of blood-brain barrier penetrating and nonpenetrating agents by statistical learning methods. J. Chem. Inf. Model. 2005, 45, 1376-1384.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1376-1384
    • Li, H.1    Yap, C.W.2    Ung, C.Y.3    Xue, Y.4    Cao, Z.W.5    Chen, Y.Z.6
  • 33
    • 33845772311 scopus 로고    scopus 로고
    • Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
    • Bazeley, P. S.; Prithivi, S.; Struble, C. A.; Povinelli, R. J.; Sem, D. S. Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: predicting affinity and conformational sampling. J. Chem. Inf. Model. 2006, 46, 2698-2708.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2698-2708
    • Bazeley, P.S.1    Prithivi, S.2    Struble, C.A.3    Povinelli, R.J.4    Sem, D.S.5
  • 34
    • 84962476960 scopus 로고    scopus 로고
    • Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks
    • Bernazzani, L.; Duce, C.; Micheli, A.; Mollica, V.; Sperduti, A.; Starita, A.; Tine, M. R. Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks. J. Chem. Inf. Model. 2006, 46, 2030-2042.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2030-2042
    • Bernazzani, L.1    Duce, C.2    Micheli, A.3    Mollica, V.4    Sperduti, A.5    Starita, A.6    Tine, M.R.7
  • 35
    • 33845760580 scopus 로고    scopus 로고
    • Applications of self-organizing neural networks in virtual screening and diversity selection
    • Selzer, P.; Ertl, P. Applications of self-organizing neural networks in virtual screening and diversity selection. J. Chem. Inf. Model. 2006, 46, 2319-2323.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2319-2323
    • Selzer, P.1    Ertl, P.2
  • 36
    • 4143122120 scopus 로고    scopus 로고
    • Classification of kinase inhibitors using a Bayesian model
    • Xia, X.; Maliski, E. G.; Gallant, P.; Rogers, D. Classification of kinase inhibitors using a Bayesian model. J. Med. Chem. 2004, 47, 4463-4470.
    • (2004) J. Med. Chem , vol.47 , pp. 4463-4470
    • Xia, X.1    Maliski, E.G.2    Gallant, P.3    Rogers, D.4
  • 37
    • 10844249112 scopus 로고    scopus 로고
    • Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D)
    • Bender, A.; Mussa, H. Y.; Gill, G. S.; Glen, R. C. Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D). J. Med. Chem. 2004, 47, 6569-6583.
    • (2004) J. Med. Chem , vol.47 , pp. 6569-6583
    • Bender, A.1    Mussa, H.Y.2    Gill, G.S.3    Glen, R.C.4
  • 38
    • 26944445752 scopus 로고    scopus 로고
    • Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naive Bayesian classifier: Limitations of the descriptor and the importance of balanced chemistry in training and test sets
    • Bender, A.; Mussa, H. Y.; Glen, R. C. Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naive Bayesian classifier: limitations of the descriptor and the importance of balanced chemistry in training and test sets. J. Biomol. Screening 2005, 10, 658-666.
    • (2005) J. Biomol. Screening , vol.10 , pp. 658-666
    • Bender, A.1    Mussa, H.Y.2    Glen, R.C.3
  • 39
    • 20444390588 scopus 로고    scopus 로고
    • A naive bayes classifier for prediction of multidrug resistance reversal activity on the basis of atom typing
    • Sun, H. A naive bayes classifier for prediction of multidrug resistance reversal activity on the basis of atom typing. J. Med. Chem. 2005, 48, 4031-4039.
    • (2005) J. Med. Chem , vol.48 , pp. 4031-4039
    • Sun, H.1
  • 40
    • 13944268698 scopus 로고    scopus 로고
    • Greater than the sum of its parts: Combining models for useful ADMET prediction
    • O'Brien, S. E.; de Groot, M. J. Greater than the sum of its parts: combining models for useful ADMET prediction. J. Med. Chem. 2005, 48, 1287-1291.
    • (2005) J. Med. Chem , vol.48 , pp. 1287-1291
    • O'Brien, S.E.1    de Groot, M.J.2
  • 41
    • 34247272948 scopus 로고    scopus 로고
    • Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem
    • Truchon, J. F.; Bayly, C. I. Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. J. Chem. Inf. Model. 2007, 47, 488-508.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 488-508
    • Truchon, J.F.1    Bayly, C.I.2
  • 42
    • 0023965741 scopus 로고    scopus 로고
    • Weininger, D. SMILES: A Chemical Language and Information System: 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
    • Weininger, D. SMILES: A Chemical Language and Information System: 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
  • 43
    • 0024664539 scopus 로고
    • SMILES 2: Algorithm for Generation of Unique SMILES Notation
    • Weininger, D.; Weininger, J. L. SMILES 2: Algorithm for Generation of Unique SMILES Notation. J. Chem. inf. Comput. Sci. 1989, 29, 97-101.
    • (1989) J. Chem. inf. Comput. Sci , vol.29 , pp. 97-101
    • Weininger, D.1    Weininger, J.L.2
  • 44
    • 0031261930 scopus 로고    scopus 로고
    • Bruno, I. J.; Cole, J. C.; Lommerse, J. P.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. IsoStar: a library of information about nonbonded interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
    • Bruno, I. J.; Cole, J. C.; Lommerse, J. P.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. IsoStar: a library of information about nonbonded interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
  • 45
    • 0038170311 scopus 로고    scopus 로고
    • Similarity metrics for ligands reflecting the similarity of the target proteins
    • Schuffenhauer, A.; Floersheim, P.; Acklin, P.; Jacoby, E. Similarity metrics for ligands reflecting the similarity of the target proteins. J. Chem. Inf. Comput. Sci. 2003, 43, 391-405.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 391-405
    • Schuffenhauer, A.1    Floersheim, P.2    Acklin, P.3    Jacoby, E.4


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