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Volumn 1, Issue 1, 2009, Pages

Application of 3D zernike descriptors to shape-based ligand similarity searching

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EID: 76749110379     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-1-19     Document Type: Article
Times cited : (56)

References (65)
  • 1
    • 10344230435 scopus 로고    scopus 로고
    • Molecular similarity: A key technique in molecular informatics
    • Molecular similarity: a key technique in molecular informatics. A Bender RC Glen, Org Biomol Chem 2004 2 3204 3218
    • (2004) Org Biomol Chem , vol.2 , pp. 3204-3218
    • Bender, A.1    Glen, R.C.2
  • 3
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity?
    • Do structurally similar molecules have similar biological activity? YC Martin JL Kofron LM Traphagen, J Med Chem 2002 45 4350 4358
    • (2002) J Med Chem , vol.45 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 4
    • 0000166488 scopus 로고    scopus 로고
    • Similarity and dissimilarity: A medicinal chemist's view
    • Similarity and dissimilarity: A medicinal chemist's view. H Kubinyi, Perspectives in Drug Discovery and Design 1998 9-11 225 252
    • (1998) Perspectives in Drug Discovery and Design , vol.9-11 , pp. 225-252
    • Kubinyi, H.1
  • 5
    • 33847207834 scopus 로고    scopus 로고
    • Molecular similarity analysis in virtual screening: Foundations, limitations and novel approaches
    • Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. H Eckert J Bajorath, Drug Discov Today 2007 12 225 233
    • (2007) Drug Discov Today , vol.12 , pp. 225-233
    • Eckert, H.1    Bajorath, J.2
  • 6
    • 84884674024 scopus 로고    scopus 로고
    • MDL Information Systems, Inc., San Leandro, CA
    • MACCS Keys. MDL Information Systems, Inc., San Leandro, CA 2009 http://www.mdl.com
    • (2009) MACCS Keys
  • 7
    • 5544290537 scopus 로고    scopus 로고
    • Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance
    • Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. A Bender HY Mussa RC Glen S Reiling, 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
  • 8
    • 0034351495 scopus 로고    scopus 로고
    • Effectiveness of retrieval in similarity searches of chemical databases: A review of performance measures
    • Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures. SJ Edgar JD Holliday P Willett, J Mol Graph Model 2000 18 343 357
    • (2000) J Mol Graph Model , vol.18 , pp. 343-357
    • Edgar, S.J.1    Holliday, J.D.2    Willett, P.3
  • 10
    • 65249092596 scopus 로고    scopus 로고
    • Similarity-based classifier using topomers to provide a knowledge base for hERG channel inhibition
    • Similarity-based classifier using topomers to provide a knowledge base for hERG channel inhibition. B Nisius AH Goller, J Chem Inf Model 2009 49 247 256
    • (2009) J Chem Inf Model , vol.49 , pp. 247-256
    • Nisius, B.1    Goller, A.H.2
  • 11
    • 10844249112 scopus 로고    scopus 로고
    • Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D)
    • DOI 10.1021/jm049611i
    • Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D). A Bender HY Mussa GS Gill RC Glen, J Med Chem 2004 47 6569 6583 (Pubitemid 39662752)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.26 , pp. 6569-6583
    • Bender, A.1    Mussa, H.Y.2    Gill, G.S.3    Glen, R.C.4
  • 13
    • 33750290951 scopus 로고    scopus 로고
    • Geometric accuracy of three-dimensional molecular overlays
    • Geometric accuracy of three-dimensional molecular overlays. Q Chen RE Higgs M Vieth, J Chem Inf Model 2006 46 1996 2002
    • (2006) J Chem Inf Model , vol.46 , pp. 1996-2002
    • Chen, Q.1    Higgs, R.E.2    Vieth, M.3
  • 15
    • 35448936472 scopus 로고    scopus 로고
    • Shapes of things: Computer modeling of molecular shape in drug discovery
    • Shapes of things: computer modeling of molecular shape in drug discovery. S Putta P Beroza, Curr Top Med Chem 2007 7 1514 1524
    • (2007) Curr Top Med Chem , vol.7 , pp. 1514-1524
    • Putta, S.1    Beroza, P.2
  • 16
    • 14944348527 scopus 로고    scopus 로고
    • A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
    • A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. TS Rush III JA Grant L Mosyak A Nicholls, 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
  • 17
    • 37249016887 scopus 로고    scopus 로고
    • Fast and efficient in silico 3D screening: Toward maximum computational efficiency of pharmacophore-based and shape-based approaches
    • Fast and efficient in silico 3D screening: toward maximum computational efficiency of pharmacophore-based and shape-based approaches. J Kirchmair S Ristic K Eder P Markt G Wolber C Laggner T Langer, J Chem Inf Model 2007 47 2182 2196
    • (2007) J Chem Inf Model , vol.47 , pp. 2182-2196
    • Kirchmair, J.1    Ristic, S.2    Eder, K.3    Markt, P.4    Wolber, G.5    Laggner, C.6    Langer, T.7
  • 19
    • 21244468757 scopus 로고    scopus 로고
    • Searching techniques for databases of two- and three-dimensional chemical structures
    • Searching techniques for databases of two- and three-dimensional chemical structures. P Willett, J Med Chem 2005 48 4183 4199
    • (2005) J Med Chem , vol.48 , pp. 4183-4199
    • Willett, P.1
  • 21
    • 2942708194 scopus 로고    scopus 로고
    • SURFCOMP: A novel graph-based approach to molecular surface comparison
    • SURFCOMP: a novel graph-based approach to molecular surface comparison. C Hofbauer H Lohninger A Aszodi, J Chem Inf Comput Sci 2004 44 837 847
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 837-847
    • Hofbauer, C.1    Lohninger, H.2    Aszodi, A.3
  • 22
    • 34547260921 scopus 로고    scopus 로고
    • Ultrafast shape recognition to search compound databases for similar molecular shapes
    • Ultrafast shape recognition to search compound databases for similar molecular shapes. PJ Ballester WG Richards, J Comput Chem 2007 28 1711 1723
    • (2007) J Comput Chem , vol.28 , pp. 1711-1723
    • Ballester, P.J.1    Richards, W.G.2
  • 23
    • 37049010775 scopus 로고    scopus 로고
    • Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment
    • Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment. BD Hudson DC Whitley MG Ford M Swain JW Essex, J Mol Model 2008 14 49 57
    • (2008) J Mol Model , vol.14 , pp. 49-57
    • Hudson, B.D.1    Whitley, D.C.2    Ford, M.G.3    Swain, M.4    Essex, J.W.5
  • 24
    • 20444385067 scopus 로고    scopus 로고
    • BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. 1. Alignment and virtual screening applications
    • BRUTUS: optimization of a grid-based similarity function for rigid-body molecular superposition. 1. Alignment and virtual screening applications. AJ Tervo T Ronkko TH Nyronen A Poso, J Med Chem 2005 48 4076 4086
    • (2005) J Med Chem , vol.48 , pp. 4076-4086
    • Tervo, A.J.1    Ronkko, T.2    Nyronen, T.H.3    Poso, A.4
  • 25
    • 0000747830 scopus 로고
    • A Gaussian description of molecular shape
    • A Gaussian description of molecular shape. JA Grant BT Pickup, J Phys Chem 1995 99 3503 3510
    • (1995) J Phys Chem , vol.99 , pp. 3503-3510
    • Grant, J.A.1    Pickup, B.T.2
  • 26
    • 0034182176 scopus 로고    scopus 로고
    • Quadratic shape descriptors. 1. Rapid superposition of dissimilar molecules using geometrically invariant surface descriptors
    • Quadratic shape descriptors. 1. Rapid superposition of dissimilar molecules using geometrically invariant surface descriptors. BB Goldman WT Wipke, J Chem Inf Comput Sci 2000 40 644 658
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 644-658
    • Goldman, B.B.1    Wipke, W.T.2
  • 27
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Analytical molecular surface calculation. ML Connolly, J Appl Cryst 1983 16 548 558
    • (1983) J Appl Cryst , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 28
    • 0027976930 scopus 로고
    • Molecular surface representations by sparse critical points
    • Molecular surface representations by sparse critical points. SL Lin R Nussinov D Fischer HJ Wolfson, Proteins 1994 18 94 101
    • (1994) Proteins , vol.18 , pp. 94-101
    • Lin, S.L.1    Nussinov, R.2    Fischer, D.3    Wolfson, H.J.4
  • 30
    • 0000720929 scopus 로고    scopus 로고
    • Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces
    • Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. DW Ritchie J Graham, J Comp Chem 1999 20 383 395
    • (1999) J Comp Chem , vol.20 , pp. 383-395
    • Ritchie, D.W.1    Graham, J.2
  • 31
    • 19544389524 scopus 로고    scopus 로고
    • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. RJ Morris RJ Najmanovich A Kahraman JM Thornton, Bioinformatics 2005 21 2347 2355
    • (2005) Bioinformatics , vol.21 , pp. 2347-2355
    • Morris, R.J.1    Najmanovich, R.J.2    Kahraman, A.3    Thornton, J.M.4
  • 32
    • 41549147243 scopus 로고    scopus 로고
    • SHEF: A vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces
    • SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces. W Cai J Xu X Shao V Leroux A Beautrait B Maigret, J Mol Model 2008 14 393 401
    • (2008) J Mol Model , vol.14 , pp. 393-401
    • Cai, W.1    Xu, J.2    Shao, X.3    Leroux, V.4    Beautrait, A.5    Maigret, B.6
  • 34
    • 68549104171 scopus 로고    scopus 로고
    • Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors
    • Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors. V Venkatraman L Sael D Kihara, Cell Biochem Biophys 2009 54 23 32
    • (2009) Cell Biochem Biophys , vol.54 , pp. 23-32
    • Venkatraman, V.1    Sael, L.2    Kihara, D.3
  • 35
    • 0345735309 scopus 로고    scopus 로고
    • Shape signatures: A new approach to computer-aided ligand- and receptor-based drug design
    • Shape signatures: a new approach to computer-aided ligand- and receptor-based drug design. RJ Zauhar G Moyna L Tian Z Li WJ Welsh, J Med Chem 2003 46 5674 5690
    • (2003) J Med Chem , vol.46 , pp. 5674-5690
    • Zauhar, R.J.1    Moyna, G.2    Tian, L.3    Li, Z.4    Welsh, W.J.5
  • 37
    • 72149132896 scopus 로고    scopus 로고
    • Local surface shape-based protein function prediction using Zernike descriptors
    • Local surface shape-based protein function prediction using Zernike descriptors. D Kihara L Sael R Chikhi, Biophys J 2009 96 650a
    • (2009) Biophys J , vol.96
    • Kihara, D.1    Sael, L.2    Chikhi, R.3
  • 38
    • 51349090017 scopus 로고    scopus 로고
    • Fast protein tertiary structure retrieval based on global surface shape similarity
    • Fast protein tertiary structure retrieval based on global surface shape similarity. L Sael B Li D La Y Fang K Ramani R Rustamov D Kihara, Proteins 2008 72 1259 1273
    • (2008) Proteins , vol.72 , pp. 1259-1273
    • Sael, L.1    Li, B.2    La, D.3    Fang, Y.4    Ramani, K.5    Rustamov, R.6    Kihara, D.7
  • 39
    • 84862297227 scopus 로고    scopus 로고
    • Protein surface representation and comparison: New approaches in structural proteomics
    • Edited by: Chen J, Lonardi S. Boca Raton, Florida, USA: Chapman & Hall/CRC Press;
    • Protein surface representation and comparison: New approaches in structural proteomics. L Sael D Kihara, Biological Data Mining Boca Raton, Florida, USA: Chapman & Hall/CRC Press, Chen J, Lonardi S, 2009 89 109
    • (2009) Biological Data Mining , pp. 89-109
    • Sael, L.1    Kihara, D.2
  • 40
    • 50849126111 scopus 로고    scopus 로고
    • Rapid comparison of properties on protein surface
    • Rapid comparison of properties on protein surface. L Sael D La B Li R Rustamov D Kihara, Proteins 2008 73 1 10
    • (2008) Proteins , vol.73 , pp. 1-10
    • Sael, L.1    La, D.2    Li, B.3    Rustamov, R.4    Kihara, D.5
  • 41
    • 40649089098 scopus 로고    scopus 로고
    • An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison
    • An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. L Mak S Grandison RJ Morris, J Mol Graph Model 2007 26 1035 1045
    • (2007) J Mol Graph Model , vol.26 , pp. 1035-1045
    • Mak, L.1    Grandison, S.2    Morris, R.J.3
  • 42
    • 0141843591 scopus 로고    scopus 로고
    • Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
    • Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. M Hattori Y Okuno S Goto M Kanehisa, J Am Chem Soc 2003 125 11853 11865
    • (2003) J Am Chem Soc , vol.125 , pp. 11853-11865
    • Hattori, M.1    Okuno, Y.2    Goto, S.3    Kanehisa, M.4
  • 43
    • 10244276964 scopus 로고    scopus 로고
    • A structure-odour relationship study using EVA descriptors and hierarchical clustering
    • A structure-odour relationship study using EVA descriptors and hierarchical clustering. SY Takane JB Mitchell, Org Biomol Chem 2004 2 3250 3255
    • (2004) Org Biomol Chem , vol.2 , pp. 3250-3255
    • Takane, S.Y.1    Mitchell, J.B.2
  • 45
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • Benchmarking sets for molecular docking. N Huang BK Shoichet JJ Irwin, J Med Chem 2006 49 6789 6801
    • (2006) J Med Chem , vol.49 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 48
    • 0037779312 scopus 로고    scopus 로고
    • 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition
    • 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. N Canterakis, Proc 11th Scandinavian Conference on Image Analysis 1999 85 93
    • (1999) Proc 11th Scandinavian Conference on Image Analysis , pp. 85-93
    • Canterakis, N.1
  • 49
    • 0006540633 scopus 로고    scopus 로고
    • Comparing measures of sample skewness and kurtosis
    • Comparing measures of sample skewness and kurtosis. DN Joanes CA Gill, The Statistician 1998 47 183 189
    • (1998) The Statistician , vol.47 , pp. 183-189
    • Joanes, D.N.1    Gill, C.A.2
  • 50
    • 0036663707 scopus 로고    scopus 로고
    • Maximum common subgraph isomorphism algorithms for the matching of chemical structures
    • DOI 10.1023/A:1021271615909
    • Maximum common subgraph isomorphism algorithms for the matching of chemical structures. JW Raymond P Willett, J Comput Aided Mol Des 2002 16 521 533 (Pubitemid 36013605)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.7 , pp. 521-533
    • Raymond, J.W.1    Willett, P.2
  • 51
    • 84976668743 scopus 로고
    • Algorithm 457: Finding all cliques of an undirected graph
    • Algorithm 457: finding all cliques of an undirected graph. C Bron J Kerbosch, Commun ACM 1973 16 575 577
    • (1973) Commun ACM , vol.16 , pp. 575-577
    • Bron, C.1    Kerbosch, J.2
  • 52
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • ZINC - a free database of commercially available compounds for virtual screening. JJ Irwin BK Shoichet, J Chem Inf Model 2005 45 177 182
    • (2005) J Chem Inf Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 53
    • 70350001745 scopus 로고    scopus 로고
    • LigMatch: A multiple structure-based ligand matching method for 3D virtual screening
    • LigMatch: a multiple structure-based ligand matching method for 3D virtual screening. SL Kinnings RM Jackson, J Chem Inf Model 2009 49 2056 2066
    • (2009) J Chem Inf Model , vol.49 , pp. 2056-2066
    • Kinnings, S.L.1    Jackson, R.M.2
  • 54
    • 57549111678 scopus 로고    scopus 로고
    • FieldScreen: Virtual screening using molecular fields. Application to the DUD data set
    • FieldScreen: virtual screening using molecular fields. Application to the DUD data set. TJ Cheeseright MD Mackey JL Melville JG Vinter, J Chem Inf Model 2008 48 2108 2117
    • (2008) J Chem Inf Model , vol.48 , pp. 2108-2117
    • Cheeseright, T.J.1    MacKey, M.D.2    Melville, J.L.3    Vinter, J.G.4
  • 55
    • 41349122416 scopus 로고    scopus 로고
    • Optimization of CAMD techniques 3. Virtual screening enrichment studies: A help or hindrance in tool selection?
    • Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? AC Good TI Oprea, J Comput Aided Mol Des 2008 22 169 178
    • (2008) J Comput Aided Mol des , vol.22 , pp. 169-178
    • Good, A.C.1    Oprea, T.I.2
  • 56
    • 73349090203 scopus 로고    scopus 로고
    • (ver. 9.6). LLC Schrodinger, New York, NY
    • MacroModel (ver. 9.6). LLC Schrodinger, New York, NY 2008 http://www.schrodinger.com/ProductDescription.php?mID=6&sID=8&cID=0
    • (2008) MacroModel
  • 57
    • 0024578841 scopus 로고
    • New soluble-formazan assay for HIV-1 cytopathic effects: Application to high-flux screening of synthetic and natural products for AIDS-antiviral activity
    • New soluble-formazan assay for HIV-1 cytopathic effects: application to high-flux screening of synthetic and natural products for AIDS-antiviral activity. OS Weislow R Kiser DL Fine J Bader RH Shoemaker MR Boyd, J Natl Cancer Inst 1989 81 577 586
    • (1989) J Natl Cancer Inst , vol.81 , pp. 577-586
    • Weislow, O.S.1    Kiser, R.2    Fine, D.L.3    Bader, J.4    Shoemaker, R.H.5    Boyd, M.R.6
  • 58
    • 84884673082 scopus 로고    scopus 로고
    • CORINA Molecular Networks
    • CORINA. Networks Molecular, Erlangen, Germany 2009 http://www.molecular- networks.com/products/corina
    • (2009) Erlangen, Germany
  • 59
    • 0037606114 scopus 로고    scopus 로고
    • Ligand-Info, searching for similar small compounds using index profiles
    • Ligand-Info, searching for similar small compounds using index profiles. M von Grotthuss J Pas L Rychlewski, Bioinformatics 2003 19 1041 1042
    • (2003) Bioinformatics , vol.19 , pp. 1041-1042
    • Von Grotthuss, M.1    Pas, J.2    Rychlewski, L.3
  • 60
    • 84944178665 scopus 로고
    • Hierarchical grouping to optimize an objective function
    • Hierarchical grouping to optimize an objective function. J Ward, J Am Stat Ass 1963 58 236 244
    • (1963) J Am Stat Ass , vol.58 , pp. 236-244
    • Ward, J.1
  • 62
    • 26944443036 scopus 로고    scopus 로고
    • A discussion of measures of enrichment in virtual screening: Comparing the information content of descriptors with increasing levels of sophistication
    • A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication. A Bender RC Glen, J Chem Inf Model 2005 45 1369 1375
    • (2005) J Chem Inf Model , vol.45 , pp. 1369-1375
    • Bender, A.1    Glen, R.C.2
  • 63
    • 34247272948 scopus 로고    scopus 로고
    • Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem
    • Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. JF Truchon CI Bayly, 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
  • 64
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • An introduction to ROC analysis. T Fawcett, Pattern Recognition Letters 2006 27 861 874
    • (2006) Pattern Recognition Letters , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 65
    • 66249144110 scopus 로고    scopus 로고
    • Better than random? the chemotype enrichment problem
    • Better than random? The chemotype enrichment problem. MD Mackey JL Melville, J Chem Inf Model 2009 49 1154 1162
    • (2009) J Chem Inf Model , vol.49 , pp. 1154-1162
    • MacKey, M.D.1    Melville, J.L.2


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