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Volumn 26, Issue 3, 2007, Pages 622-633

Flexible 3D pharmacophores as descriptors of dynamic biological space

Author keywords

3D descriptors; Biological space; Chemical space; FEPOPS; Pharmacophore; Virtual screening

Indexed keywords

ALGORITHMS; CONFORMATIONS; CRYSTAL STRUCTURE; LIGANDS; OPTIMIZATION; PROTEINS; THREE DIMENSIONAL;

EID: 34848919746     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2007.02.005     Document Type: Article
Times cited : (44)

References (45)
  • 2
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale 10.1126/science. 278.5338.680
    • DeRisi J.L., Iyer V.R., and Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale 10.1126/science. 278.5338.680. Science 278 5338 (1997) 680-686
    • (1997) Science , vol.278 , Issue.5338 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 4
    • 0032495513 scopus 로고    scopus 로고
    • Structure of the alpha beta tubulin dimer by electron crystallography
    • Nogales E., Wolf S.G., and Downing K.H. Structure of the alpha beta tubulin dimer by electron crystallography. Nature 391 6663 (1998) 199-203
    • (1998) Nature , vol.391 , Issue.6663 , pp. 199-203
    • Nogales, E.1    Wolf, S.G.2    Downing, K.H.3
  • 5
    • 33644850985 scopus 로고    scopus 로고
    • The Dam1 kinetochore ring complex moves processively on depolymerizing microtubule ends
    • Westermann S., Wang H.W., Avila-Sakar A., Drubin D.G., Nogales E., and Barnes G. The Dam1 kinetochore ring complex moves processively on depolymerizing microtubule ends. Nature 440 7083 (2006) 565-569
    • (2006) Nature , vol.440 , Issue.7083 , pp. 565-569
    • Westermann, S.1    Wang, H.W.2    Avila-Sakar, A.3    Drubin, D.G.4    Nogales, E.5    Barnes, G.6
  • 6
    • 0037374498 scopus 로고    scopus 로고
    • The price of innovation: new estimates of drug development costs
    • DiMasi J.A., Hansen R.W., and Grabowski H.G. The price of innovation: new estimates of drug development costs. J. Health Econ. 22 2 (2003) 151-185
    • (2003) J. Health Econ. , vol.22 , Issue.2 , pp. 151-185
    • DiMasi, J.A.1    Hansen, R.W.2    Grabowski, H.G.3
  • 7
    • 0037070587 scopus 로고    scopus 로고
    • Identification of ligand binding sites on proteins using a multi-scale approach
    • Glick M., Robinson D.D., Grant G.H., and Richards W.G. Identification of ligand binding sites on proteins using a multi-scale approach. J. Am. Chem. Soc. 124 10 (2002) 2337-2344
    • (2002) J. Am. Chem. Soc. , vol.124 , Issue.10 , pp. 2337-2344
    • Glick, M.1    Robinson, D.D.2    Grant, G.H.3    Richards, W.G.4
  • 8
    • 0037057576 scopus 로고    scopus 로고
    • Docking of flexible molecules using multiscale ligand representations
    • Glick M., Grant G.H., and Richards W.G. Docking of flexible molecules using multiscale ligand representations. J. Med. Chem. 45 21 (2002) 4639-4646
    • (2002) J. Med. Chem. , vol.45 , Issue.21 , pp. 4639-4646
    • Glick, M.1    Grant, G.H.2    Richards, W.G.3
  • 10
    • 0346962971 scopus 로고    scopus 로고
    • Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions
    • Deng Z., Chuaqui C., and Singh J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem. 47 2 (2004) 337-344
    • (2004) J. Med. Chem. , vol.47 , Issue.2 , pp. 337-344
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 11
    • 10344230435 scopus 로고    scopus 로고
    • Molecular similarity: a key technique in molecular informatics
    • Bender A., and Glen R.C. Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem. 2 22 (2004) 3204-3218
    • (2004) Org. Biomol. Chem. , vol.2 , Issue.22 , pp. 3204-3218
    • Bender, A.1    Glen, R.C.2
  • 12
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity?
    • Martin Y.C., Kofron J.L., and Traphagen L.M. Do structurally similar molecules have similar biological activity?. J. Med. Chem. 45 19 (2002) 4350-4358
    • (2002) J. Med. Chem. , vol.45 , Issue.19 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 13
    • 9744222830 scopus 로고    scopus 로고
    • A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes
    • Jenkins J.L., Glick M., and Davies J.W. A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes. J. Med. Chem. 47 25 (2004) 6144-6159
    • (2004) J. Med. Chem. , vol.47 , Issue.25 , pp. 6144-6159
    • Jenkins, J.L.1    Glick, M.2    Davies, J.W.3
  • 14
    • 0000629279 scopus 로고
    • Mathematical contributions to the theory of evolution. III. Regression, heredity, and panmixia
    • Pearson K. Mathematical contributions to the theory of evolution. III. Regression, heredity, and panmixia. Philos. Trans. R. Soc. Lond. A Math. Phys. Eng. Sci. 187 (1896) 253-318
    • (1896) Philos. Trans. R. Soc. Lond. A Math. Phys. Eng. Sci. , vol.187 , pp. 253-318
    • Pearson, K.1
  • 15
    • 33750994920 scopus 로고    scopus 로고
    • Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors
    • Nettles J.H., Jenkins J.L., Bender A., Deng Z., Davies J.W., and Glick M. Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. J. Med. Chem. 49 (2006) 6802-6810
    • (2006) J. Med. Chem. , vol.49 , pp. 6802-6810
    • Nettles, J.H.1    Jenkins, J.L.2    Bender, A.3    Deng, Z.4    Davies, J.W.5    Glick, M.6
  • 17
    • 14944348527 scopus 로고    scopus 로고
    • A shape-based 3D scaffold hopping method and its application to a bacterial protein-protein interaction
    • Rush III T.S., Grant J.A., Mosyak L., and Nicholls A. A shape-based 3D scaffold hopping method and its application to a bacterial protein-protein interaction. J. Med. Chem. 48 5 (2005) 1489-1495
    • (2005) J. Med. Chem. , vol.48 , Issue.5 , pp. 1489-1495
    • Rush III, T.S.1    Grant, J.A.2    Mosyak, L.3    Nicholls, A.4
  • 18
    • 34848928077 scopus 로고    scopus 로고
    • Pipeline Pilot, SciTegic, San Diego, CA, 2005.
  • 19
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges
    • Gasteiger J., and Marsili M. Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 36 22 (1980) 3219-3228
    • (1980) Tetrahedron , vol.36 , Issue.22 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 20
    • 0000262640 scopus 로고    scopus 로고
    • A new atom-additive method for calculating partition coefficients
    • Wang R., Fu Y., and Lai L. A new atom-additive method for calculating partition coefficients. J. Chem. Inf. Model. 37 3 (1997) 615-621
    • (1997) J. Chem. Inf. Model. , vol.37 , Issue.3 , pp. 615-621
    • Wang, R.1    Fu, Y.2    Lai, L.3
  • 24
    • 34848883863 scopus 로고    scopus 로고
    • MDL Public Keys, Elsevier MDL Inc., San Ramon, CA, 2001.
  • 25
    • 34848897448 scopus 로고    scopus 로고
    • Molecular Operating Environment (MOE), Computational Computing Group, Montreal, Canada, 2006.
  • 26
    • 0042891852 scopus 로고    scopus 로고
    • Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)
    • Lakdawala A., Wang M., Nevins N., Liotta D.C., Rusinska-Roszak D., Lozynski M., and Snyder J.P. Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study). BMC Chem. Biol. 1 1 (2001) 2
    • (2001) BMC Chem. Biol. , vol.1 , Issue.1 , pp. 2
    • Lakdawala, A.1    Wang, M.2    Nevins, N.3    Liotta, D.C.4    Rusinska-Roszak, D.5    Lozynski, M.6    Snyder, J.P.7
  • 27
    • 0033596738 scopus 로고    scopus 로고
    • Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase
    • Narayana N., Diller T.C., Koide K., Bunnage M.E., Nicolaou K.C., Brunton L.L., Xuong N.H., Ten Eyck L.F., and Taylor S.S. Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase. Biochemistry 38 8 (1999) 2367-2376
    • (1999) Biochemistry , vol.38 , Issue.8 , pp. 2367-2376
    • Narayana, N.1    Diller, T.C.2    Koide, K.3    Bunnage, M.E.4    Nicolaou, K.C.5    Brunton, L.L.6    Xuong, N.H.7    Ten Eyck, L.F.8    Taylor, S.S.9
  • 29
    • 33745391215 scopus 로고    scopus 로고
    • Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases
    • Nidhi, Glick M., Davies J.W., and Jenkins J.L. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J. Chem. Inf. Model. 46 3 (2006) 1124-1133
    • (2006) J. Chem. Inf. Model. , vol.46 , Issue.3 , pp. 1124-1133
    • Nidhi1    Glick, M.2    Davies, J.W.3    Jenkins, J.L.4
  • 31
    • 0034065350 scopus 로고    scopus 로고
    • Computational methods for the structural alignment of molecules
    • Lemmen C., and Lengauer T. Computational methods for the structural alignment of molecules. J. Comput. Aided Mol. Des. 14 3 (2000) 215-232
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , Issue.3 , pp. 215-232
    • Lemmen, C.1    Lengauer, T.2
  • 32
    • 0002212887 scopus 로고    scopus 로고
    • HipHop: pharmacophores based on multiple common-feature alignments
    • Guner O.F. (Ed), International University Line, La Jolla
    • Clement O.O., and Mehl A.T. HipHop: pharmacophores based on multiple common-feature alignments. In: Guner O.F. (Ed). Pharmacophore Perception, Development and Use in Drug Design (2000), International University Line, La Jolla 69-84
    • (2000) Pharmacophore Perception, Development and Use in Drug Design , pp. 69-84
    • Clement, O.O.1    Mehl, A.T.2
  • 33
    • 0013122190 scopus 로고    scopus 로고
    • What We Did Right and What We Missed
    • Guner O.F. (Ed), International University Line, La Jolla
    • Martin Y.C.D. What We Did Right and What We Missed. In: Guner O.F. (Ed). Pharmacophore Perception, Development and Use in Drug Design (2000), International University Line, La Jolla 51-68
    • (2000) Pharmacophore Perception, Development and Use in Drug Design , pp. 51-68
    • Martin, Y.C.D.1
  • 34
    • 0036706746 scopus 로고    scopus 로고
    • A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP
    • Patel Y., Gillet V.J., Bravi G., and Leach A.R. A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP. J. Comput. Aided Mol. Des. 16 8/9 (2002) 653-681
    • (2002) J. Comput. Aided Mol. Des. , vol.16 , Issue.8-9 , pp. 653-681
    • Patel, Y.1    Gillet, V.J.2    Bravi, G.3    Leach, A.R.4
  • 35
    • 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
    • Dixon S.L., Smondyrev A.M., Knoll E.H., Rao S.N., Shaw D.E., and 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. 20 10-11 (2006) 647-671
    • (2006) J. Comput. Aided Mol. Des. , 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
  • 36
    • 3843053396 scopus 로고    scopus 로고
    • The binding mode of epothilone A on alpha, beta-tubulin by electron crystallography
    • Nettles J.H., Li H., Cornett B., Krahn J.M., Snyder J.P., and Downing K.H. The binding mode of epothilone A on alpha, beta-tubulin by electron crystallography. Science 305 5685 (2004) 866-869
    • (2004) Science , vol.305 , Issue.5685 , pp. 866-869
    • Nettles, J.H.1    Li, H.2    Cornett, B.3    Krahn, J.M.4    Snyder, J.P.5    Downing, K.H.6
  • 37
    • 33244482848 scopus 로고    scopus 로고
    • Enrichment of high-throughput screening data with increasing levels of noise using support vector machines, recursive partitioning, and laplacian-modified naive bayesian classifiers
    • Glick M., Jenkins J.L., Nettles J.H., Hitchings H., and Davies J.W. Enrichment of high-throughput screening data with increasing levels of noise using support vector machines, recursive partitioning, and laplacian-modified naive bayesian classifiers. J. Chem. Inf. Model. 46 1 (2006) 193-200
    • (2006) J. Chem. Inf. Model. , vol.46 , Issue.1 , pp. 193-200
    • Glick, M.1    Jenkins, J.L.2    Nettles, J.H.3    Hitchings, H.4    Davies, J.W.5
  • 38
    • 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., and Schuffenhauer A. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org. Biomol. Chem. 2 22 (2004) 3256-3266
    • (2004) Org. Biomol. Chem. , vol.2 , Issue.22 , 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
  • 40
    • 0032488013 scopus 로고    scopus 로고
    • FLEXS: a method for fast flexible ligand superposition
    • Lemmen C., Lengauer T., and Klebe G. FLEXS: a method for fast flexible ligand superposition. J. Med. Chem. 41 23 (1998) 4502-4520
    • (1998) J. Med. Chem. , vol.41 , Issue.23 , pp. 4502-4520
    • Lemmen, C.1    Lengauer, T.2    Klebe, G.3
  • 41
    • 0033523672 scopus 로고    scopus 로고
    • Scaffold-hopping by topological pharmacophore search: a contribution to virtual screening
    • Schneider G., Neidhart W., Giller T., and Schmid G. Scaffold-hopping by topological pharmacophore search: a contribution to virtual screening. Angew. Chem. Int. Ed. Engl. 38 19 (1999) 2894-2896
    • (1999) Angew. Chem. Int. Ed. Engl. , vol.38 , Issue.19 , pp. 2894-2896
    • Schneider, G.1    Neidhart, W.2    Giller, T.3    Schmid, G.4
  • 42
    • 0033969620 scopus 로고    scopus 로고
    • Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition
    • Jain A.N. Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition. J. Comput. Aided Mol. Des. 14 2 (2000) 199-213
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , Issue.2 , pp. 199-213
    • Jain, A.N.1
  • 43
    • 0036010701 scopus 로고    scopus 로고
    • dbtop: Topomer similarity searching of conventional structure databases
    • Cramer R.D., Jilek R.J., and Andrews K.M. dbtop: Topomer similarity searching of conventional structure databases. J. Mol. Graph. Modell. 20 6 (2002) 447-462
    • (2002) J. Mol. Graph. Modell. , vol.20 , Issue.6 , pp. 447-462
    • Cramer, R.D.1    Jilek, R.J.2    Andrews, K.M.3
  • 44
    • 20844457125 scopus 로고    scopus 로고
    • Variable selection and model validation of 2D and 3D molecular descriptors
    • Nicholls A., MacCuish N.E., and MacCuish J.D. Variable selection and model validation of 2D and 3D molecular descriptors. J. Comput. Aided Mol. Des. 18 7-9 (2004) 451-474
    • (2004) J. Comput. Aided Mol. Des. , vol.18 , Issue.7-9 , pp. 451-474
    • Nicholls, A.1    MacCuish, N.E.2    MacCuish, J.D.3
  • 45
    • 13844320566 scopus 로고    scopus 로고
    • LigandScout: 3D pharmacophores derived from protein-bound ligands and their use as virtual screening filters
    • Wolber G., and Langer T. LigandScout: 3D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model. 45 1 (2005) 160-169
    • (2005) J. Chem. Inf. Model. , vol.45 , Issue.1 , pp. 160-169
    • Wolber, G.1    Langer, T.2


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