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Volumn 50, Issue 5, 2010, Pages 771-784

Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS;

EID: 77952780755     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100062n     Document Type: Article
Times cited : (283)

References (53)
  • 4
    • 0342645323 scopus 로고    scopus 로고
    • Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection
    • Brown, R. D.; Martin, Y. C. Use of Structure-Activity Data to Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection J. Chem. Inf. Comput. Sci. 1996, 36, 572-584
    • (1996) J. Chem. Inf. Comput. Sci. , vol.36 , pp. 572-584
    • Brown, R.D.1    Martin, Y.C.2
  • 5
    • 5244364312 scopus 로고    scopus 로고
    • The information content of 2d and 3d structural descriptors relevant to ligand-receptor bond
    • Brown, R. D.; Martin, Y. C. The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Bond J. Chem. Inf. Comput. Sci. 1997, 37, 1-9
    • (1997) J. Chem. Inf. Comput. Sci. , vol.37 , pp. 1-9
    • Brown, R.D.1    Martin, Y.C.2
  • 6
    • 0030943408 scopus 로고    scopus 로고
    • Selecting optimally diverse compounds from structure databases: A validation study of two-dimensional and three-dimensional molecular descriptors
    • Matter, H. Selecting Optimally Diverse Compounds from Structure Databases: A Validation Study of Two-Dimensional and Three-Dimensional Molecular Descriptors J. Med. Chem. 1997, 40, 1219-1229
    • (1997) J. Med. Chem. , vol.40 , pp. 1219-1229
    • Matter, H.1
  • 7
    • 0032572819 scopus 로고    scopus 로고
    • Can we learn to distinguish between "drug-like" and nondrug-like" molecules?
    • Ajay; Walters, W. P.; Murcko, M. A. Can We Learn to Distinguish between "Drug-like" and Nondrug-like" Molecules? J. Med. Chem. 1998, 41, 3314-3324
    • (1998) J. Med. Chem. , vol.41 , pp. 3314-3324
    • Ajay1    Walters, W.P.2    Murcko, M.A.3
  • 8
    • 0035829402 scopus 로고    scopus 로고
    • One-dimensional molecular representations and similarity calculations: Methodology and validation
    • Dixon, S. L.; Merz, K. M., Jr. One-Dimensional Molecular Representations and Similarity Calculations: Methodology and Validation J. Med. Chem. 2001, 44, 3795-3809
    • (2001) J. Med. Chem. , vol.44 , pp. 3795-3809
    • Dixon, S.L.1    Merz Jr., K.M.2
  • 11
    • 0028412035 scopus 로고
    • FLOG: A system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure
    • Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. FLOG: A System to Select Quasi-Flexible Ligands Complementary to a Receptor of Known Three-Dimensional Structure J. Comput.-Aided Mol. Des. 1994, 8, 153-174
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 153-174
    • Miller, M.D.1    Kearsley, S.K.2    Underwood, D.J.3    Sheridan, R.P.4
  • 12
    • 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
  • 15
    • 0001462919 scopus 로고
    • Three-dimensional pharmacophore pattern searching
    • Springer-Verlag: Berlin, Germany
    • Gund, P., Three-Dimensional Pharmacophore Pattern Searching. In, Progress in Molecular and Subcellular Biology; Hahn, F. E., Ed.; Springer-Verlag: Berlin, Germany, 1977; Vol. 5, pp 117 - 143.
    • (1977) Progress in Molecular and Subcellular Biology , vol.5 , pp. 117-143
    • Gund, P.1    Hahn, F.E.2
  • 16
    • 0000719721 scopus 로고
    • Use of flexible queries for searching conformationally flexible molecules in databases of three-dimensional structures
    • Güner, O. F.; Henry, D. R.; Pearlman, R. S. Use of Flexible Queries for Searching Conformationally Flexible Molecules in Databases of Three-Dimensional Structures J. Chem. Inf. Comput. Sci. 1992, 32, 101-109
    • (1992) J. Chem. Inf. Comput. Sci. , vol.32 , pp. 101-109
    • Güner, O.F.1    Henry, D.R.2    Pearlman, R.S.3
  • 17
    • 0028256928 scopus 로고
    • Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational searching algorithms for flexible searching
    • Clark, D. E.; Jones, G.; Willett, P. Pharmacophoric Pattern Matching in Files of Three-Dimensional Chemical Structures: Comparison of Conformational Searching Algorithms for Flexible Searching J. Chem. Inf. Comput. Sci. 1994, 34, 197-206
    • (1994) J. Chem. Inf. Comput. Sci. , vol.34 , pp. 197-206
    • Clark, D.E.1    Jones, G.2    Willett, P.3
  • 21
    • 77952755931 scopus 로고    scopus 로고
    • version 3.0; OpenEye Scientific Software: Sante Fe, NM, 2009
    • ROCS, version 3.0; OpenEye Scientific Software: Sante Fe, NM, 2009.
    • ROCS
  • 22
    • 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
  • 23
    • 0001232509 scopus 로고    scopus 로고
    • On the properties of bit string-based measures of chemical similarity
    • Flower, D. R. On the Properties of Bit String-Based Measures of Chemical Similarity J. Chem. Inf. Comput. Sci. 1998, 38, 379-386
    • (1998) J. Chem. Inf. Comput. Sci. , vol.38 , pp. 379-386
    • Flower, D.R.1
  • 24
    • 0033615007 scopus 로고    scopus 로고
    • The hidden component of size in two-dimensional fragment descriptors: Side effects on sampling in bioactive libraries
    • Dixon, S. L.; Koehler, R. T. The Hidden Component of Size in Two-Dimensional Fragment Descriptors: Side Effects on Sampling in Bioactive Libraries J. Med. Chem. 1999, 42, 2887-2900
    • (1999) J. Med. Chem. , vol.42 , pp. 2887-2900
    • Dixon, S.L.1    Koehler, R.T.2
  • 25
    • 0032149905 scopus 로고    scopus 로고
    • Feature trees: A new molecular measure based on tree matching
    • Rarey, M.; Dixon, J. S. Feature Trees: A New Molecular Measure Based on Tree Matching J. Comput.-Aided Mol. Des. 1998, 12, 471-490
    • (1998) J. Comput.-Aided Mol. Des. , vol.12 , pp. 471-490
    • Rarey, M.1    Dixon, J.S.2
  • 26
    • 0033127029 scopus 로고    scopus 로고
    • Pharmacophore fingerprinting. 1. Application to QSAR and focused library design
    • McGregor, M. J.; Muskal, S. M. Pharmacophore Fingerprinting. 1. Application to QSAR and Focused Library Design J. Chem. Inf. Comput. Sci. 1999, 39, 569-574
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 569-574
    • McGregor, M.J.1    Muskal, S.M.2
  • 28
    • 0033598416 scopus 로고    scopus 로고
    • Prospective identification of biologically active structures by topomer shape similarity searching
    • Cramer, R. D.; Poss, M. A.; Hersmeier, M. A.; Caulfield, T. J.; Kowala, M. C.; Valentine, M. T. Prospective Identification of Biologically Active Structures by Topomer Shape Similarity Searching J. Med. Chem. 1999, 42, 3919-3933
    • (1999) J. Med. Chem. , vol.42 , pp. 3919-3933
    • Cramer, R.D.1    Poss, M.A.2    Hersmeier, M.A.3    Caulfield, T.J.4    Kowala, M.C.5    Valentine, M.T.6
  • 30
    • 77952758008 scopus 로고    scopus 로고
    • version 1.2; Schrödinger L.L.C.: New York, NY, 2009
    • Canvas, version 1.2; Schrödinger L.L.C.: New York, NY, 2009.
    • Canvas
  • 31
    • 0036827080 scopus 로고    scopus 로고
    • Performance of similarity measures in 2D fragment-based similarity searching: Comparison of structural descriptors and similarity coefficients
    • Chen, X.; Reynolds, C. H. Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients J. Chem. Inf. Comput. Sci. 2002, 42, 1407-1414
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 1407-1414
    • Chen, X.1    Reynolds, C.H.2
  • 32
    • 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
  • 33
    • 33846020557 scopus 로고    scopus 로고
    • Similarity metrics and descriptor spaces - Which combinations to choose
    • Glen, R. C.; Adams, S. E. Similarity Metrics and Descriptor Spaces-Which Combinations to Choose QSAR Comb. Sci. 2006, 25, 1133-1142
    • (2006) QSAR Comb. Sci. , vol.25 , pp. 1133-1142
    • Glen, R.C.1    Adams, S.E.2
  • 34
    • 33751246188 scopus 로고    scopus 로고
    • Similarity-based virtual screening using 2d fingerprints
    • Willet, P. Similarity-Based Virtual Screening Using 2D Fingerprints Drug Discovery Today 2006, 11, 1046-1053
    • (2006) Drug Discovery Today , vol.11 , pp. 1046-1053
    • Willet, P.1
  • 35
    • 53349090841 scopus 로고    scopus 로고
    • MDL Information Systems/Symyx: Santa Clara, CA, 2005
    • MDL Drug Data Report; MDL Information Systems/Symyx: Santa Clara, CA, 2005.
    • MDL Drug Data Report
  • 36
    • 85019788301 scopus 로고    scopus 로고
    • MDL Information Systems/Symyx: Santa Clara, CA, 1984
    • MACCS-II; MDL Information Systems/Symyx: Santa Clara, CA, 1984.
    • MACCS-II
  • 37
    • 77952783781 scopus 로고    scopus 로고
    • version 4.9; Daylight Chemical Systems, Inc.: Aliso Viejo, CA, 2008
    • Daylight Fingerprint Toolkit, version 4.9; Daylight Chemical Systems, Inc.: Aliso Viejo, CA, 2008.
    • Daylight Fingerprint Toolkit
  • 38
    • 77952762796 scopus 로고    scopus 로고
    • version 4.4; Tripos L.P.: St. Louis, MO, 2003
    • Unity, version 4.4; Tripos L.P.: St. Louis, MO, 2003.
    • Unity
  • 39
    • 77952775934 scopus 로고    scopus 로고
    • version 5.3.2; ChemAxon: Budapest, Hungary, 2010
    • GenerateMD, version 5.3.2; ChemAxon: Budapest, Hungary, 2010.
    • GenerateMD
  • 40
    • 0004117251 scopus 로고    scopus 로고
    • Daylight Chemical Systems, Inc.: Aliso Viejo, CA, 2008
    • Daylight Theory Manual; Daylight Chemical Systems, Inc.: Aliso Viejo, CA, 2008.
    • Daylight Theory Manual
  • 41
    • 0002046725 scopus 로고    scopus 로고
    • Dissimilarity-based compound selection techniques
    • Lajiness, M. S. Dissimilarity-based Compound Selection Techniques Perspect. Drug Discovery Des. 1997, 7/8, 65-84
    • (1997) Perspect. Drug Discovery Des. , vol.78 , pp. 65-84
    • Lajiness, M.S.1
  • 42
    • 26944503021 scopus 로고    scopus 로고
    • Using extended-connectivity fingerprints with laplacian-modified bayesian analysis in high-throughput screening follow-up
    • Rogers, D.; Brown, R. D.; Hahn, M. Using Extended-Connectivity Fingerprints with Laplacian-Modified Bayesian Analysis in High-Throughput Screening Follow-up J. Biomol. Screening 2005, 10, 682-686
    • (2005) J. Biomol. Screening , vol.10 , pp. 682-686
    • Rogers, D.1    Brown, R.D.2    Hahn, M.3
  • 43
    • 0000293407 scopus 로고
    • The generation of a unique machine description for chemical structure - A technique developed at chemical abstracts service
    • Morgan, H. L. The Generation of a Unique Machine Description for Chemical Structure-A Technique Developed at Chemical Abstracts Service J. Chem. Doc. 1965, 5, 107-113
    • (1965) J. Chem. Doc. , vol.5 , pp. 107-113
    • Morgan, H.L.1
  • 44
    • 33845379303 scopus 로고
    • Atom pairs as molecular features in structure-activity studies: Definitions and applications
    • Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom Pairs as Molecular Features in Structure-Activity Studies: Definitions and Applications J. Chem. Inf. Comput. Sci. 1985, 25, 65-73
    • (1985) J. Chem. Inf. Comput. Sci. , vol.25 , pp. 65-73
    • Carhart, R.E.1    Smith, D.H.2    Venkataraghavan, R.3
  • 45
    • 0003076470 scopus 로고
    • Topological torsions: A new molecular descriptor for sar applications. Comparison with other descriptors
    • Nilakantan, R.; Bauman, N.; Dixon, J. S.; Venkataraghavan, R. Topological Torsions: A New Molecular Descriptor for SAR Applications. Comparison with Other Descriptors J. Chem. Inf. Comput. Sci. 1987, 27, 82-85
    • (1987) J. Chem. Inf. Comput. Sci. , vol.27 , pp. 82-85
    • Nilakantan, R.1    Bauman, N.2    Dixon, J.S.3    Venkataraghavan, R.4
  • 46
    • 1842690601 scopus 로고    scopus 로고
    • Molecular similarity searching using atom environments, information-based feature selection, and a naïve bayesian classifier
    • Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier J. Chem. Inf. Comput. Sci. 2004, 44, 170-178
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 170-178
    • Bender, A.1    Mussa, H.Y.2    Glen, R.C.3    Reiling, S.4
  • 47
    • 5544290537 scopus 로고    scopus 로고
    • Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance
    • Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 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
  • 49
    • 77952761225 scopus 로고    scopus 로고
    • version 8.1.1; Tripos L.P.: St. Louis, MO, 2009
    • Sybyl, version 8.1.1; Tripos L.P.: St. Louis, MO, 2009.
    • Sybyl
  • 52
    • 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. Comput. Sci. 2007, 47, 448-508
    • (2007) J. Chem. Inf. Comput. Sci. , vol.47 , pp. 448-508
    • Truchon, J.-F.1    Bayly, C.I.2
  • 53
    • 37249011239 scopus 로고    scopus 로고
    • Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval
    • Baldi, P.; Benz, R. W.; Hirschberg, D. S.; Swamidass, S. J. Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval J. Chem. Inf. Model. 2007, 47, 2098-2109
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 2098-2109
    • Baldi, P.1    Benz, R.W.2    Hirschberg, D.S.3    Swamidass, S.J.4


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