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Volumn 14, Issue 6, 2011, Pages 488-499

Pharmacophore modeling methods in focused library selection-applications in the context of a new classification scheme

Author keywords

Alignment; Feature abstraction; Feature comparison; Feature selection; Focused library; Lead identification; Pharmacophore

Indexed keywords

CALCIUM CHANNEL BLOCKING AGENT; CANNABINOID; MITOGEN ACTIVATED PROTEIN KINASE 14; TUBERCULOSTATIC AGENT;

EID: 79957993168     PISSN: 13862073     EISSN: 18755402     Source Type: Journal    
DOI: 10.2174/138620711795767820     Document Type: Article
Times cited : (13)

References (109)
  • 2
    • 0001008140 scopus 로고    scopus 로고
    • Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1997)
    • ed.; Bristol, J. A., Ed. Academic Press
    • Wermuth, C. G.; Ganellin, C. R.; Lindberg, P.; Mitscher, L. A. Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1997). In Annu. Rep. Med. Chem., 33 ed.; Bristol, J. A., Ed. Academic Press: 1998; pp 385-395.
    • (1998) Annu. Rep. Med. Chem. , vol.33 , pp. 385-395
    • Wermuth, C.G.1    Ganellin, C.R.2    Lindberg, P.3    Mitscher, L.A.4
  • 5
    • 0035003352 scopus 로고    scopus 로고
    • 3-D pharmacophores in drug discovery
    • DOI 10.2174/1381612013397843
    • (b) Mason, J. S.; Good, A. C.; Martin, E. J. 3-D pharmacophores in drug discovery. Curr. Pharm. Des., 2001, 7(7), 567-97; (Pubitemid 32427655)
    • (2001) Current Pharmaceutical Design , vol.7 , Issue.7 , pp. 567-597
    • Mason, J.S.1    Good, A.C.2    Martin, E.J.3
  • 6
    • 0041488802 scopus 로고    scopus 로고
    • Pharmacophore discovery - Lessons learned
    • (c) Van Drie, J. H. Pharmacophore Discovery - Lessons Learned. Curr. Pharm. Des., 2003, 9(20), 1649-64;
    • (2003) Curr. Pharm. Des. , vol.9 , Issue.20 , pp. 1649-1664
    • Van Drie, J.H.1
  • 8
    • 84906460724 scopus 로고    scopus 로고
    • Pharmacophore modeling: 1 - Methods
    • Taylor, J. B.; Triggle, D. J.; Mason, J. S., Eds. Elsevier: Amsterdam
    • (e) Martin, Y. C. Pharmacophore Modeling: 1 - Methods. In Comprehensive Medicinal Chemistry II, Taylor, J. B.; Triggle, D. J.; Mason, J. S., Eds. Elsevier: Amsterdam, 2007; Vol. 4, pp 119-147;
    • (2007) Comprehensive Medicinal Chemistry II , vol.4 , pp. 119-147
    • Martin, Y.C.1
  • 9
    • 84906481419 scopus 로고    scopus 로고
    • Pharmacophore modeling: 2 - Applications
    • Taylor, J. B.; Triggle, D. J.; Mason, J. S., Eds. Elsevier: Amsterdam
    • (f) Martin, Y. C. Pharmacophore Modeling: 2 - Applications. In Comprehensive Medicinal Chemistry II, Taylor, J. B.; Triggle, D. J.; Mason, J. S., Eds. Elsevier: Amsterdam, 2007; Vol. 4, pp 515-536;
    • (2007) Comprehensive Medicinal Chemistry II , vol.4 , pp. 515-536
    • Martin, Y.C.1
  • 10
    • 77249106566 scopus 로고    scopus 로고
    • Three-dimensional pharmacophore methods in drug discovery
    • (g) Leach, A. R.; Gillet, V. J.; Lewis, R. A.; Taylor, R. Three-dimensional pharmacophore methods in drug discovery. J. Med. Chem., 2010, 53(2), 539-558;
    • (2010) J. Med. Chem. , vol.53 , Issue.2 , pp. 539-558
    • Leach, A.R.1    Gillet, V.J.2    Lewis, R.A.3    Taylor, R.4
  • 11
    • 77954818699 scopus 로고    scopus 로고
    • Pharmacophore modeling and applications in drug discovery: Challenges and recent advances
    • (h) Yang, S. Y., Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov. Today, 2010, 15 (11/12), 444-450.
    • (2010) Drug Discov. Today , vol.15 , Issue.11-12 , pp. 444-450
    • Yang, S.Y.1
  • 12
    • 0034444471 scopus 로고    scopus 로고
    • Comments on the design of chemical libraries for screening
    • DOI 10.1023/A:1011326914800
    • Villar, H. O.; Koehler, R. T. Comments on the design of chemical libraries for screening. Mol. Divers., 2000, 5(1), 13-24. (Pubitemid 32422188)
    • (2000) Molecular Diversity , vol.5 , Issue.1 , pp. 13-24
    • Villar, H.O.1    Koehler, R.T.2
  • 14
    • 33845868822 scopus 로고    scopus 로고
    • PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
    • DOI 10.1007/s10822-006-9087-6
    • Dixon, S. L.; Smondyrev, A. M.; Knoll, E. H.; Rao, S. N.; Shaw, D. E.; Friesner, R. A. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J. Comput. Aided Mol. Des., 2006, 20 (10-11), 647-671. (Pubitemid 46023928)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.10-11 , pp. 647-671
    • Dixon, S.L.1    Smondyrev, A.M.2    Knoll, E.H.3    Rao, S.N.4    Shaw, D.E.5    Friesner, R.A.6
  • 15
    • 79953185645 scopus 로고    scopus 로고
    • Daylight Chemical Information Systems: Santa Fe, New Mexico
    • SMARTS Theory Manual, Daylight Chemical Information Systems: Santa Fe, New Mexico, 2008.
    • (2008) SMARTS Theory Manual
  • 16
    • 79957994771 scopus 로고    scopus 로고
    • Tripos Inc.
    • (a) SYBYL-X, Tripos Inc.: 2010;
    • (2010) SYBYL-X
  • 17
    • 0028337945 scopus 로고
    • Flexible 3D searching: The directed tweak technique
    • (b) Hurst, T. Flexible 3D searching: The directed tweak technique. J. Chem. Inf. Comput. Sci., 1994, 34(1), 190-196;
    • (1994) J. Chem. Inf. Comput. Sci. , vol.34 , Issue.1 , pp. 190-196
    • Hurst, T.1
  • 18
    • 0028256928 scopus 로고
    • Pharmacophoric pattern matching in files of threedimensional chemical structures: Comparison of conformationalsearching algorithms for flexible searching
    • (c) Clark, D. E.; Jones, G.; Willett, P.; Kenny, P. W.; Glen, R. C. Pharmacophoric pattern matching in files of threedimensional chemical structures: Comparison of conformationalsearching algorithms for flexible searching. J. Chem. Inf. Comput. Sci., 1994, 34(1), 197-206.
    • (1994) J. Chem. Inf. Comput. Sci. , vol.34 , Issue.1 , pp. 197-206
    • Clark, D.E.1    Jones, G.2    Willett, P.3    Kenny, P.W.4    Glen, R.C.5
  • 20
    • 58149119670 scopus 로고    scopus 로고
    • SYBYL line notation (SLN): A single notation to represent chemical structures, queries, reactions, and virtual libraries
    • (b) Homer, R. W.; Swanson, J.; Jilek, R. J.; Hurst, T.; Clark, R. D. SYBYL line notation (SLN): a single notation to represent chemical structures, queries, reactions, and virtual libraries. J. Chem. Inf. Model., 2008, 48(12), 2294-2307.
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.12 , pp. 2294-2307
    • Homer, R.W.1    Swanson, J.2    Jilek, R.J.3    Hurst, T.4    Clark, R.D.5
  • 21
    • 37249062877 scopus 로고    scopus 로고
    • Accelrys Inc.
    • (a) Discovery Studio, Accelrys Inc.: 2010;
    • (2010) Discovery Studio
  • 24
    • 79957979822 scopus 로고
    • 9th Noordwijkerhout Camerino Medicinal Chemistry Symposium, Noordwijkerhout, The Netherlands, Noordwijkerhout, The Netherlands
    • Berezin, S.; Greene, J.; Kahn, S.; Ku, S.; Teig, S. In CHM: A Chemically expressive database query language, 9th Noordwijkerhout Camerino Medicinal Chemistry Symposium, Noordwijkerhout, The Netherlands, Noordwijkerhout, The Netherlands, 1993.
    • (1993) CHM: A Chemically Expressive Database Query Language
    • Berezin, S.1    Greene, J.2    Kahn, S.3    Ku, S.4    Teig, S.5
  • 25
    • 34247263219 scopus 로고    scopus 로고
    • A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): Theory and application
    • DOI 10.1021/ci600253e
    • Baroni, M.; Cruciani, G.; Sciabola, S.; Perruccio, F.; Mason, J. S. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): theory and application. J. Chem. Inf. Model., 2007, 47(2), 279-294. (Pubitemid 46615933)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.2 , pp. 279-294
    • Baroni, M.1    Cruciani, G.2    Sciabola, S.3    Perruccio, F.4    Mason, J.S.5
  • 26
    • 0035974531 scopus 로고    scopus 로고
    • Application of structure-based focusing to the estrogen receptor
    • DOI 10.1002/jcc.1060
    • Kirchhoff, P. D.; Brown, R.; Kahn, S.; Waldman, M.; Venkatachalam, C. M. Application of structure-based focusing to the estrogen receptor. J. Comput. Chem., 2001, 22(10), 993-1003. (Pubitemid 32614371)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.10 , pp. 993-1003
    • Kirchhoff, P.D.1
  • 27
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • DOI 10.1021/jm00145a002
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem., 1985, 28(7), 849-57. (Pubitemid 15012490)
    • (1985) Journal of Medicinal Chemistry , vol.28 , Issue.7 , pp. 849-857
    • Goodford, P.J.1
  • 28
    • 79957994512 scopus 로고    scopus 로고
    • Cepos InSilico Limited
    • ParaSurf, Cepos InSilico Limited: 2010.
    • (2010) ParaSurf
  • 29
    • 73749087803 scopus 로고    scopus 로고
    • Molecular fields in drug discovery: Getting old or reaching maturity?
    • Cross, S.; Cruciani, G. Molecular fields in drug discovery: getting old or reaching maturity? Drug Discov. Today, 2010, 15 (1-2), 23-32.
    • (2010) Drug Discov. Today , vol.15 , Issue.1-2 , pp. 23-32
    • Cross, S.1    Cruciani, G.2
  • 30
    • 79957997989 scopus 로고    scopus 로고
    • Chemical Computing Group
    • MOE, Chemical Computing Group: 2010.
    • (2010) MOE
  • 31
    • 0001383234 scopus 로고    scopus 로고
    • HypoGen: An automated system for generating 3D predictive pharmacophore models
    • Güner, O. F., Ed. International University Line: la Jolla, California
    • Li, H.; Sutter, J.; Hoffmann, R. HypoGen: An Automated System for Generating 3D Predictive Pharmacophore Models. In Pharmacophore Perception, Development, and use in Drug Design, Güner, O. F., Ed. International University Line: la Jolla, California, 2000; pp 171-189.
    • (2000) Pharmacophore Perception, Development, and use in Drug Design , pp. 171-189
    • Li, H.1    Sutter, J.2    Hoffmann, R.3
  • 32
    • 9744222830 scopus 로고    scopus 로고
    • A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes
    • DOI 10.1021/jm049654z
    • Jenkins, J. L.; Glick, M.; Davies, J. W. A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes. J. Med. Chem., 2004, 47(25), 6144-6159. (Pubitemid 39587240)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.25 , pp. 6144-6159
    • Jenkins, J.L.1    Glick, M.2    Davies, J.W.3
  • 33
    • 0027548454 scopus 로고
    • A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists
    • Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists. J. Comput. Aided Mol. Des., 1993, 7(1), 83-102.
    • (1993) J. Comput. Aided Mol. Des. , vol.7 , Issue.1 , pp. 83-102
    • Martin, Y.C.1    Bures, M.G.2    Danaher, E.A.3    DeLazzer, J.4    Lico, I.5    Pavlik, P.A.6
  • 34
    • 0029444383 scopus 로고
    • A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
    • Jones, G.; Willett, P.; Glen, R. C. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J Comput Aided Mol. Des., 1995, 9(6), 532-549.
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , Issue.6 , pp. 532-549
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 36
    • 0024725804 scopus 로고
    • ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures
    • Van Drie, J. H.; Weininger, D.; Martin, Y. C. ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures. J. Comput. Aided Mol. Des., 1989, 3(3), 225-251.
    • (1989) J. Comput. Aided Mol. Des. , vol.3 , Issue.3 , pp. 225-251
    • Van Drie, J.H.1    Weininger, D.2    Martin, Y.C.3
  • 37
    • 0001204208 scopus 로고
    • Computer-Assisted Pharmacophore Identification
    • Kubinyi, H., Ed. ESCOM Science Publishers: Netherlands
    • Golender, V.; Vorpagel, E. Computer-Assisted Pharmacophore Identification. In 3D QSAR in Drug Design: Theory, Methods and Applications, Kubinyi, H., Ed. ESCOM Science Publishers: Netherlands, 1993; pp 137-149.
    • (1993) 3D QSAR in Drug Design: Theory, Methods and Applications , pp. 137-149
    • Golender, V.1    Vorpagel, E.2
  • 39
    • 0002574413 scopus 로고    scopus 로고
    • CLEW: The generation of pharmacophore hypotheses through machine learning
    • Dolata, D. P.; Parrill, A. L.; Walters, W. P. CLEW: The generation of pharmacophore hypotheses through machine learning. SAR QSAR Environ. Res., 1998, 9(1), 53-81.
    • (1998) SAR QSAR Environ. Res. , vol.9 , Issue.1 , pp. 53-81
    • Dolata, D.P.1    Parrill, A.L.2    Walters, W.P.3
  • 41
    • 0042196198 scopus 로고    scopus 로고
    • Fast 3D molecular superposition and similarity search in databases of flexible molecules
    • DOI 10.1023/A:1024503712135
    • Kramer, A.; Horn, H. W.; Rice, J. E. Fast 3D molecular superposition and similarity search in databases of flexible molecules. J. Comput.-Aided Mol. Des., 2003, 17(1), 13-38. (Pubitemid 36939538)
    • (2003) Journal of Computer-Aided Molecular Design , vol.17 , Issue.1 , pp. 13-38
    • Kramer, A.1    Horn, H.W.2    Rice, J.E.3
  • 43
    • 72849140490 scopus 로고    scopus 로고
    • Using a staged multi-objective optimization approach to find selective pharmacophore models
    • Springer Netherlands
    • (b) Clark, R. D.; Abrahamian, E. Using a staged multi-objective optimization approach to find selective pharmacophore models. In J. Comput.-Aided Mol. Des., Springer Netherlands: 2009; Vol. 23, pp 765-771.
    • (2009) J. Comput.-Aided Mol. Des. , vol.23 , pp. 765-771
    • Clark, R.D.1    Abrahamian, E.2
  • 44
    • 79958013449 scopus 로고    scopus 로고
    • We classify GALAHAD as an alignment-based method, as this is how the comparison of test ligands is performed with respect to the model. However, the use of 3D fingerprints is a key step in conformer selection when building the models
    • We classify GALAHAD as an alignment-based method, as this is how the comparison of test ligands is performed with respect to the model. However, the use of 3D fingerprints is a key step in conformer selection when building the models.
  • 45
    • 13844320566 scopus 로고    scopus 로고
    • LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters
    • DOI 10.1021/ci049885e
    • (a) Wolber, G.; Langer, T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model., 2005, 45(1), 160-169; (Pubitemid 40736968)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.1 , pp. 160-169
    • Wolber, G.1    Langer, T.2
  • 46
    • 37649009919 scopus 로고    scopus 로고
    • Moleculepharmacophore superpositioning and pattern matching in computational drug design
    • (b) Wolber, G.; Seidel, T.; Bendix, F.; Langer, T. Moleculepharmacophore superpositioning and pattern matching in computational drug design. Drug Discov. Today, 2008, 13 (1-2), 23-29.
    • (2008) Drug Discov. Today , vol.13 , Issue.1-2 , pp. 23-29
    • Wolber, G.1    Seidel, T.2    Bendix, F.3    Langer, T.4
  • 47
    • 61949359014 scopus 로고    scopus 로고
    • Common pharmacophore identification using frequent clique detection algorithm
    • Podolyan, Y.; Karypis, G. Common pharmacophore identification using frequent clique detection algorithm. J. Chem. Inf. Model., 2008, 49(1), 13-21.
    • (2008) J. Chem. Inf. Model. , vol.49 , Issue.1 , pp. 13-21
    • Podolyan, Y.1    Karypis, G.2
  • 48
    • 15844366918 scopus 로고    scopus 로고
    • Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques
    • DOI 10.1007/s10822-004-5523-7
    • Cottrell, S. J.; Gillet, V. J.; Taylor, R.; Wilton, D. J., Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques. J. Comput.-Aided Mol. Des., 2004, 18(11), 665-682. (Pubitemid 40425038)
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , Issue.11 , pp. 665-682
    • Cottrell, S.J.1    Gillet, V.J.2    Taylor, R.3    Wilton, D.J.4
  • 49
    • 52049125711 scopus 로고    scopus 로고
    • Pharao: Pharmacophore alignment and optimization
    • Taminau, J.; Thijs, G.; De Winter, H. Pharao: pharmacophore alignment and optimization. J. Mol. Graphics Model., 2008, 27(2), 161-169.
    • (2008) J. Mol. Graphics Model. , vol.27 , Issue.2 , pp. 161-169
    • Taminau, J.1    Thijs, G.2    De Winter, H.3
  • 50
    • 70449729379 scopus 로고    scopus 로고
    • Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules
    • Springer Verlag
    • Inbar, Y.; Schneidman-Duhovny, D.; Dror, O.; Nussinov, R.; Wolfson, H. J., Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules. In Proc. of RECOMB 2007, Springer Verlag: 2007; Vol. 3692, pp 423-434.
    • (2007) Proc. of RECOMB 2007 , vol.3692 , pp. 423-434
    • Inbar, Y.1    Schneidman-Duhovny, D.2    Dror, O.3    Nussinov, R.4    Wolfson, H.J.5
  • 52
    • 0031997218 scopus 로고    scopus 로고
    • Pharmacophore discovery using the inductive logic programming system PROGOL
    • Finn, P.; Muggleton, S.; Page, D.; Srinivasan, A. Pharmacophore discovery using the inductive logic programming system PROGOL. Machine Learning, 1998, 30(2), 241-270.
    • (1998) Machine Learning , vol.30 , Issue.2 , pp. 241-270
    • Finn, P.1    Muggleton, S.2    Page, D.3    Srinivasan, A.4
  • 53
    • 34250801603 scopus 로고    scopus 로고
    • QUASI: A novel method for simultaneous superposition of multiple flexible ligands and virtual screening using partial similarity
    • DOI 10.1021/ci6003338
    • Todorov, N. P.; Alberts, I. L.; de Esch, I. J.; Dean, P. M. QUASI: a novel method for simultaneous superposition of multiple flexible ligands and virtual screening using partial similarity. J. Chem. Inf. Model., 2007, 47(3), 1007-1020. (Pubitemid 46973716)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.3 , pp. 1007-1020
    • Todorov, N.P.1    Alberts, I.L.2    De Esch, I.J.P.3    Dean, P.M.4
  • 55
    • 0033193464 scopus 로고    scopus 로고
    • Automated pharmacophore identification for large chemical data sets
    • Chen, X.; Rusinko, A., 3rd.; Tropsha, A.; Young, S. S. Automated pharmacophore identification for large chemical data sets. J. Chem. Inf. Comput. Sci., 1999, 39(5), 887-896.
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , Issue.5 , pp. 887-896
    • Chen, X.1    Rusinko III, A.2    Tropsha, A.3    Young, S.S.4
  • 56
    • 37849034064 scopus 로고    scopus 로고
    • Atomic property fields: Generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR
    • Totrov, M. Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem. Biol. Drug Des., 2008, 71(1), 15-27.
    • (2008) Chem. Biol. Drug Des. , vol.71 , Issue.1 , pp. 15-27
    • Totrov, M.1
  • 58
    • 41549117981 scopus 로고    scopus 로고
    • A self-organizing algorithm for molecular alignment and pharmacophore development
    • DOI 10.1002/jcc.20854
    • Bandyopadhyay, D.; Agrafiotis, D. K. A self-organizing algorithm for molecular alignment and pharmacophore development. J. Comput. Chem., 2008, 29(6), 965-982. (Pubitemid 351473693)
    • (2008) Journal of Computational Chemistry , vol.29 , Issue.6 , pp. 965-982
    • Agrafiotis, D.K.1    Bandyopadhyay, D.2
  • 59
    • 79957998274 scopus 로고    scopus 로고
    • Treweren Consultants Ltd.
    • THINK, Treweren Consultants Ltd.: 2010.
    • (2010) THINK
  • 60
    • 33646227896 scopus 로고    scopus 로고
    • Molecular field extrema as descriptors of biological activity: Definition and validation
    • (a) Cheeseright, T.; Mackey, M.; Rose, S.; Vinter, A. Molecular field extrema as descriptors of biological activity: definition and validation. J. Chem. Inf. Model., 2006, 46(2), 665-676;
    • (2006) J. Chem. Inf. Model. , vol.46 , Issue.2 , pp. 665-676
    • Cheeseright, T.1    Mackey, M.2    Rose, S.3    Vinter, A.4
  • 61
    • 57549111678 scopus 로고    scopus 로고
    • FieldScreen: Virtual screening using molecular fields. Application to the DUD data set
    • (b) Cheeseright, T. J.; Mackey, M. D.; Melville, J. L.; Vinter, J. G. FieldScreen: virtual screening using molecular fields. Application to the DUD data set. J. Chem. Inf. Model., 2008, 48(11), 2108-2117.
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.11 , pp. 2108-2117
    • Cheeseright, T.J.1    Mackey, M.D.2    Melville, J.L.3    Vinter, J.G.4
  • 62
    • 47349106302 scopus 로고    scopus 로고
    • FieldChopper, a new tool for automatic model generation and virtual screening based on molecular fields
    • Kalliokoski, T.; Ronkko, T.; Poso, A. FieldChopper, a new tool for automatic model generation and virtual screening based on molecular fields. J. Chem. Inf. Model., 2008, 48(6), 1131-1137.
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.6 , pp. 1131-1137
    • Kalliokoski, T.1    Ronkko, T.2    Poso, A.3
  • 63
    • 0037431383 scopus 로고    scopus 로고
    • Field interaction and geometrical overlap: A new simplex and experimental design based computational procedure for superposing small ligand molecules
    • DOI 10.1021/jm0210616
    • Melani, F.; Gratteri, P.; Adamo, M.; Bonaccini, C. Field interaction and geometrical overlap: a new simplex and experimental design based computational procedure for superposing small ligand molecules. J. Med. Chem., 2003, 46(8), 1359-1371. (Pubitemid 36512700)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.8 , pp. 1359-1371
    • Melani, F.1    Gratteri, P.2    Adamo, M.3    Bonaccini, C.4
  • 64
    • 33745584385 scopus 로고    scopus 로고
    • GBPM: GRID-based pharmacophore model: Concept and application studies to protein-protein recognition
    • DOI 10.1093/bioinformatics/btl115
    • Ortuso, F.; Langer, T.; Alcaro, S. GBPM: GRID-based pharmacophore model: concept and application studies to proteinprotein recognition. Bioinformatics, 2006, 22(12), 1449-1455. (Pubitemid 43985315)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1449-1455
    • Ortuso, F.1    Langer, T.2    Alcaro, S.3
  • 65
    • 33845727607 scopus 로고    scopus 로고
    • Pocket v.2: Further developments on receptor-based pharmacophore modeling
    • DOI 10.1021/ci600246s
    • Chen, J.; Lai, L. Pocket v. 2: further developments on receptorbased pharmacophore modeling. J. Chem. Inf. Model., 2006, 46(6), 2684-2691. (Pubitemid 46008137)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2684-2691
    • Chen, J.1    Lai, L.2
  • 66
    • 33845791138 scopus 로고    scopus 로고
    • Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes
    • DOI 10.1021/ci6002416
    • Bonachera, F.; Parent, B.; Barbosa, F.; Froloff, N.; Horvath, D. Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes. J. Chem. Inf. Model., 2006, 46(6), 2457-2477. (Pubitemid 46008118)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2457-2477
    • Bonachera, F.1    Parent, B.2    Barbosa, F.3    Froloff, N.4    Horvath, D.5
  • 67
    • 65249167021 scopus 로고    scopus 로고
    • Relevance of feature combinations for similarity searching using general or activity class-directed molecular fingerprints
    • Lounkine, E.; Hu, Y.; Batista, J.; Bajorath, J. Relevance of feature combinations for similarity searching using general or activity class-directed molecular fingerprints. J. Chem. Inf. Model., 2009, 49(3), 561-570.
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.3 , pp. 561-570
    • Lounkine, E.1    Hu, Y.2    Batista, J.3    Bajorath, J.4
  • 69
    • 0001642977 scopus 로고
    • Conformational freedom in 3-D databases. 1. Techniques
    • Murrall, N. W.; Davies, E. K. Conformational freedom in 3-D databases. 1. Techniques. J. Chem. Inf. Comput. Sci., 1990, 30(3), 312-316.
    • (1990) J. Chem. Inf. Comput. Sci. , vol.30 , Issue.3 , pp. 312-316
    • Murrall, N.W.1    Davies, E.K.2
  • 70
    • 77952772341 scopus 로고    scopus 로고
    • Extended-connectivity fingerprints
    • Rogers, D.; Hahn, M. Extended-connectivity fingerprints. J. Chem. Inf. Model., 2010, 50(5), 742-754.
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.5 , pp. 742-754
    • Rogers, D.1    Hahn, M.2
  • 71
    • 44449143540 scopus 로고    scopus 로고
    • Flexophore, a new versatile 3D pharmacophore descriptor that considers molecular flexibility
    • DOI 10.1021/ci700359j
    • von Korff, M.; Freyss, J.; Sander, T. Flexophore, a new versatile 3D pharmacophore descriptor that considers molecular flexibility. J. Chem. Inf. Model., 2008, 48(4), 797-810. (Pubitemid 351757745)
    • (2008) Journal of Chemical Information and Modeling , vol.48 , Issue.4 , pp. 797-810
    • Von Korff, M.1    Freyss, J.2    Sander, T.3
  • 72
    • 65249134411 scopus 로고    scopus 로고
    • Simple idea to generate fragment and pharmacophore descriptors and their implications in chemical informatics
    • Catana, C. Simple idea to generate fragment and pharmacophore descriptors and their implications in chemical informatics. J. Chem. Inf. Model., 2009, 49(3), 543-548.
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.3 , pp. 543-548
    • Catana, C.1
  • 74
    • 0034351494 scopus 로고    scopus 로고
    • Oriented substituent pharmacophore PRopErtY space (OSPPREYS): A substituent-based calculation that describes combinatorial library products better than the corresponding product-based calculation
    • Martin, E. J.; Hoeffel, T. J. Oriented substituent pharmacophore PRopErtY space (OSPPREYS): a substituent-based calculation that describes combinatorial library products better than the corresponding product-based calculation. J. Mol. Graphics Model. 2000, 18 (4-5), 383-403.
    • (2000) J. Mol. Graphics Model , vol.18 , Issue.4-5 , pp. 383-403
    • Martin, E.J.1    Hoeffel, T.J.2
  • 75
    • 33646855259 scopus 로고    scopus 로고
    • Accelrys Inc
    • Pipeline Pilot, Accelrys Inc: 2010.
    • (2010) Pipeline Pilot
  • 76
    • 75749126524 scopus 로고    scopus 로고
    • Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening
    • Sato, T.; Honma, T.; Yokoyama, S. Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening. J. Chem. Inf. Model., 2010, 50(1), 170-185.
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.1 , pp. 170-185
    • Sato, T.1    Honma, T.2    Yokoyama, S.3
  • 79
    • 79957990535 scopus 로고    scopus 로고
    • ChemAxon Kft
    • Screen, ChemAxon Kft: 2010.
    • (2010) Screen
  • 80
    • 0346962971 scopus 로고    scopus 로고
    • Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions
    • DOI 10.1021/jm030331x
    • Deng, Z.; Chuaqui, C.; Singh, J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional proteinligand binding interactions. J. Med. Chem., 2004, 47(2), 337-344. (Pubitemid 38057878)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.2 , pp. 337-344
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 81
    • 4444275159 scopus 로고    scopus 로고
    • Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening
    • DOI 10.1021/jm031139y
    • Renner, S.; Schneider, G. Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening. J. Med. Chem., 2004, 47(19), 4653-4664. (Pubitemid 39195556)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.19 , pp. 4653-4664
    • Renner, S.1    Schneider, G.2
  • 82
    • 0037363560 scopus 로고    scopus 로고
    • Efficient generation, storage, and manipulation of fully flexible pharmacophore multiplets and their use in 3-D similarity searching
    • Abrahamian, E.; Fox, P. C.; Naerum, L.; Christensen, I. T.; Thogersen, H.; Clark, R. D. Efficient generation, storage, and manipulation of fully flexible pharmacophore multiplets and their use in 3-D similarity searching. J. Chem. Inf. Comput. Sci., 2003, 43(2), 458-468.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , Issue.2 , pp. 458-468
    • Abrahamian, E.1    Fox, P.C.2    Naerum, L.3    Christensen, I.T.4    Thogersen, H.5    Clark, R.D.6
  • 83
    • 0035950118 scopus 로고    scopus 로고
    • Measuring molecular similarity and diversity: Total pharmacophore diversity
    • DOI 10.1021/jm010036h
    • Makara, G. M. Measuring molecular similarity and diversity: total pharmacophore diversity. J. Med. Chem., 2001, 44(22), 3563-3571. (Pubitemid 33026663)
    • (2001) Journal of Medicinal Chemistry , vol.44 , Issue.22 , pp. 3563-3571
    • Makara, G.M.1
  • 84
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr
    • Kabsch, W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. Sect. A: Found. Crystallogr., 1978, 34(5), 827-828.
    • (1978) Sect. A: Found. Crystallogr. , vol.34 , Issue.5 , pp. 827-828
    • Kabsch, W.1
  • 85
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B.; Richards, F. M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 1971, 55(3), 379-400.
    • (1971) J. Mol. Biol. , vol.55 , Issue.3 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 86
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography. Acta Crystallogr
    • Collaborative Computational Project Number 4
    • Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D. Biol. Crystallogr., 1994, 50 (Pt 5), 760-763.
    • (1994) Sect. D. Biol. Crystallogr. , vol.50 , Issue.5 PART , pp. 760-763
  • 87
    • 0028695270 scopus 로고
    • Extended electron distributions applied to the molecular mechanics of some intermolecular interactions
    • (a) Vinter, J. G. Extended electron distributions applied to the molecular mechanics of some intermolecular interactions. J. Comput. Aided Mol. Des., 1994, 8(6), 653-668;
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , Issue.6 , pp. 653-668
    • Vinter, J.G.1
  • 88
    • 0030255292 scopus 로고    scopus 로고
    • Extended electron distributions applied to the molecular mechanics of some intermolecular interactions. II. Organic complexes
    • (b) Vinter, J. G. Extended electron distributions applied to the molecular mechanics of some intermolecular interactions. II. Organic complexes. J. Comput. Aided Mol. Des., 1996, 10(5), 417-426. (Pubitemid 126712438)
    • (1996) Journal of Computer-Aided Molecular Design , vol.10 , Issue.5 , pp. 417-426
    • Vinter, J.G.1
  • 89
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • DOI 10.1021/jm00145a002
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem., 1985, 28(7), 849-857. (Pubitemid 15012490)
    • (1985) Journal of Medicinal Chemistry , vol.28 , Issue.7 , pp. 849-857
    • Goodford, P.J.1
  • 90
    • 43049151814 scopus 로고    scopus 로고
    • Identification of novel cannabinoid CB1 receptor antagonists by using virtual screening with a pharmacophore model
    • DOI 10.1021/jm701519h
    • Wang, H.; Duffy, R. A.; Boykow, G. C.; Chackalamannil, S.; Madison, V. S. Identification of novel cannabinoid CB1 receptor antagonists by using virtual screening with a pharmacophore model. J. Med. Chem., 2008, 51(8), 2439-2446. (Pubitemid 351628505)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.8 , pp. 2439-2446
    • Wang, H.1    Duffy, R.A.2    Boykow, G.C.3    Chackalamannil, S.4    Madison, V.S.5
  • 91
    • 84855205915 scopus 로고    scopus 로고
    • Schrödinger LLC
    • MacroModel, Schrödinger LLC: 2010.
    • (2010) MacroModel
  • 92
    • 79957990002 scopus 로고    scopus 로고
    • Accelrys Inc.
    • MDDR database, Accelrys Inc.: 2010.
    • (2010) MDDR Database
  • 93
    • 61949212798 scopus 로고    scopus 로고
    • Knowledge based identification of potent antitubercular compounds using structure based virtual screening and structure interaction fingerprints
    • Kumar, A.; Chaturvedi, V.; Bhatnagar, S.; Sinha, S.; Siddiqi, M. I. Knowledge based identification of potent antitubercular compounds using structure based virtual screening and structure interaction fingerprints. J. Chem. Inf. Model., 2008, 49(1), 35-42.
    • (2008) J. Chem. Inf. Model. , vol.49 , Issue.1 , pp. 35-42
    • Kumar, A.1    Chaturvedi, V.2    Bhatnagar, S.3    Sinha, S.4    Siddiqi, M.I.5
  • 94
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol., 1996, 261(3), 470-489. (Pubitemid 26335901)
    • (1996) Journal of Molecular Biology , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 97
    • 0025330414 scopus 로고
    • Diltiazem. A reappraisal of its pharmacological properties and therapeutic use
    • (a) Buckley, M. M.; Grant, S. M.; Goa, K. L.; McTavish, D.; Sorkin, E. M. Diltiazem. A reappraisal of its pharmacological properties and therapeutic use. Drugs, 1990, 39(5), 757-806;
    • (1990) Drugs , vol.39 , Issue.5 , pp. 757-806
    • Buckley, M.M.1    Grant, S.M.2    Goa, K.L.3    McTavish, D.4    Sorkin, E.M.5
  • 99
    • 0036682190 scopus 로고    scopus 로고
    • Cardiovascular characterization of [1,4]thiazino[3,4-c][1,2,4]oxadiazol- 1-one derivatives: Selective myocardial calcium channel modulators
    • DOI 10.1021/jm020815d
    • Budriesi, R.; Cosimelli, B.; Ioan, P.; Lanza, C. Z.; Spinelli, D.; Chiarini, A. Cardiovascular characterization of [1,4]thiazino[3,4-c][1,2,4] oxadiazol-1-one derivatives: selective myocardial calcium channel modulators. J. Med. Chem., 2002, 45(16), 3475-3481. (Pubitemid 34824035)
    • (2002) Journal of Medicinal Chemistry , vol.45 , Issue.16 , pp. 3475-3481
    • Budriesi, R.1    Cosimelli, B.2    Ioan, P.3    Lanza, C.Z.4    Spinelli, D.5    Chiarini, A.6
  • 100
    • 0019512619 scopus 로고
    • Comparative effects of three calcium antagonists, diltiazem, verapamil and nifedipine, on the sinoatrial and atrioventricular nodes. Experimental and clinical studies
    • Kawai, C.; Konishi, T.; Matsuyama, E.; Okazaki, H. Comparative effects of three calcium antagonists, diltiazem, verapamil and nifedipine, on the sinoatrial and atrioventricular nodes. Experimental and clinical studies. Circulation, 1981, 63(5), 1035-1042. (Pubitemid 11106369)
    • (1981) Circulation , vol.63 , Issue.5 , pp. 1035-1042
    • Kawai, C.1    Konishi, T.2    Matsuyama, E.3    Okazaki, H.4
  • 101
    • 4644308675 scopus 로고    scopus 로고
    • Therapeutic drugs that behave as mechanism-based inhibitors of cytochrome P450 3A4
    • DOI 10.2174/1389200043335450
    • Zhou, S.; Chan, E.; Lim, L. Y.; Boelsterli, U. A.; Li, S. C.; Wang, J.; Zhang, Q.; Huang, M.; Xu, A. Therapeutic drugs that behave as mechanism-based inhibitors of cytochrome P450 3A4. Curr. Drug Metab., 2004, 5(5), 415-442. (Pubitemid 39276605)
    • (2004) Current Drug Metabolism , vol.5 , Issue.5 , pp. 415-442
    • Zhou, S.1    Chan, E.2    Lim, L.Y.3    Boelsterli, U.A.4    Li, S.C.5    Wang, J.6    Zhang, Q.7    Huang, M.8    Xu, A.9
  • 102
    • 79957971562 scopus 로고    scopus 로고
    • The overall library consisted of 198160 compounds from Sigma-Aldrich Inc. 47401
    • The overall library consisted of 198160 compounds from Sigma-Aldrich Inc. (http://www.sigmaaldrich.com), 47401
  • 103
    • 79958017439 scopus 로고    scopus 로고
    • from Key Organics Ltd. 83286
    • from Key Organics Ltd. (http://www.keyorganics.ltd.uk), 83286
  • 104
    • 79957977388 scopus 로고    scopus 로고
    • from Maybridge Chemicals, 5017
    • from Maybridge Chemicals (http://www.maybridge.com), 5017
  • 105
    • 79957972142 scopus 로고    scopus 로고
    • from Menai Organics Ltd
    • from Menai Organics Ltd. (http://www.ryansci.com)
  • 106
    • 79957974517 scopus 로고    scopus 로고
    • 8548 from Peakdale Molecular
    • and 8548 from Peakdale Molecular (http://www.peakdale.co.uk).


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