메뉴 건너뛰기




Volumn 52, Issue 11, 2012, Pages 2884-2901

Similarity coefficients for binary chemoinformatics data: Overview and extended comparison using simulated and real data sets

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

EID: 84870022937     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300261r     Document Type: Article
Times cited : (163)

References (74)
  • 2
    • 77649220192 scopus 로고    scopus 로고
    • Current trends in ligand-based virtual screening: Molecular representations, data mining methods, new application areas, and performance evaluation
    • Geppert, H.; Vogt, M.; Bajorath, J. Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation J. Chem. Inf. Model. 2010, 50, 205-216
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 205-216
    • Geppert, H.1    Vogt, M.2    Bajorath, J.3
  • 3
    • 78650352933 scopus 로고    scopus 로고
    • Quo vadis, virtual screening? A comprehensive survey of prospective applications
    • Rippenhausen, P.; Nisius, B.; Peltason, L.; Bajorath, J. Quo vadis, virtual screening? A comprehensive survey of prospective applications J. Med. Chem. 2010, 53, 8461-8467
    • (2010) J. Med. Chem. , vol.53 , pp. 8461-8467
    • Rippenhausen, P.1    Nisius, B.2    Peltason, L.3    Bajorath, J.4
  • 4
    • 77950503976 scopus 로고    scopus 로고
    • Virtual screening: An endless staircase?
    • Schneider, G. Virtual screening: an endless staircase? Nat. Rev. Drug Discov. 2010, 9, 273-276
    • (2010) Nat. Rev. Drug Discov. , vol.9 , pp. 273-276
    • Schneider, G.1
  • 6
    • 57849168939 scopus 로고    scopus 로고
    • Similarity methods in chemoinformatics
    • Willett, P. Similarity methods in chemoinformatics Ann. Rev. Inform. Sci. Technol. 2009, 43, 3-71
    • (2009) Ann. Rev. Inform. Sci. Technol. , vol.43 , pp. 3-71
    • Willett, P.1
  • 7
    • 61949166066 scopus 로고    scopus 로고
    • How similar are similarity searching methods? A principal components analysis of molecular descriptor space
    • Bender, A.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C. K.; Glick, M.; Davies, J. W. How similar are similarity searching methods? A principal components analysis of molecular descriptor space J. Chem. Inf. Model. 2009, 49, 108-119
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 108-119
    • Bender, A.1    Jenkins, J.L.2    Scheiber, J.3    Sukuru, S.C.K.4    Glick, M.5    Davies, J.W.6
  • 9
    • 34447515227 scopus 로고    scopus 로고
    • Chemical similarity searches: When is complexity justified?
    • DOI 10.1517/17460441.2.4.423
    • Sheridan, R. P. Chemical similarity searches: when is complexity justified? Expert Opin. Drug Discov. 2007, 2, 423-430 (Pubitemid 47073070)
    • (2007) Expert Opinion on Drug Discovery , vol.2 , Issue.4 , pp. 423-430
    • Sheridan, R.P.1
  • 10
    • 77956276766 scopus 로고    scopus 로고
    • Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods
    • Duan, J.; Dixon, S. L.; Lowrie, J. F.; Sherman, W. Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods J. Mol. Graph. Mod. 2010, 29, 157-170
    • (2010) J. Mol. Graph. Mod. , vol.29 , pp. 157-170
    • Duan, J.1    Dixon, S.L.2    Lowrie, J.F.3    Sherman, W.4
  • 11
    • 0036249270 scopus 로고    scopus 로고
    • Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings
    • Holliday, J. D.; Hu, C.-Y.; Willett, P. Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings Combin. Chem. High-Throughput Screening 2002, 5, 155-166 (Pubitemid 34475167)
    • (2002) Combinatorial Chemistry and High Throughput Screening , vol.5 , Issue.2 , pp. 155-166
    • Holliday, J.D.1    Hu, C.-Y.2    Willett, P.3
  • 12
    • 77952780755 scopus 로고    scopus 로고
    • Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments
    • Sastry, M.; Lowrie, J. F.; Dixon, S. L.; Sherman, W. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments J. Chem. Inf. Model. 2010, 50, 771-748
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 771-748
    • Sastry, M.1    Lowrie, J.F.2    Dixon, S.L.3    Sherman, W.4
  • 13
    • 21844514245 scopus 로고
    • Comparing resemblance measures
    • Batagelj, V.; Bren, M. Comparing resemblance measures J. Classif. 1995, 12, 73-90
    • (1995) J. Classif. , vol.12 , pp. 73-90
    • Batagelj, V.1    Bren, M.2
  • 14
    • 0001115709 scopus 로고
    • Binary (presence-absence) similarity coefficients
    • Cheetham, A. H.; Hazel, J. E. Binary (presence-absence) similarity coefficients J. Paleontol. 1969, 43, 1130-1136
    • (1969) J. Paleontol. , vol.43 , pp. 1130-1136
    • Cheetham, A.H.1    Hazel, J.E.2
  • 15
    • 0020451042 scopus 로고
    • Coefficients of Association and Similarity, based on Binary (Presence-Absence) data: An Evaluation
    • Hubalek, Z. Coefficients of Association and Similarity, based on Binary (Presence-Absence) data: An Evaluation Biol. Rev. 1982, 57, 669-689
    • (1982) Biol. Rev. , vol.57 , pp. 669-689
    • Hubalek, Z.1
  • 19
    • 84861512073 scopus 로고    scopus 로고
    • Similarity-based data mining in files of two-dimensional chemical structures using fingerprint-based measures of molecular resemblance
    • Willett, P. Similarity-based data mining in files of two-dimensional chemical structures using fingerprint-based measures of molecular resemblance WIRES Data Mining Knowledge Disc. 2011, 1, 241-251
    • (2011) WIRES Data Mining Knowledge Disc. , vol.1 , pp. 241-251
    • Willett, P.1
  • 20
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal, R. R.; Michener, C. D. A statistical method for evaluating systematic relationships Univ. Kansas. Sci. Bull. 1958, 38, 1409-1438
    • (1958) Univ. Kansas. Sci. Bull. , vol.38 , pp. 1409-1438
    • Sokal, R.R.1    Michener, C.D.2
  • 21
    • 84950632109 scopus 로고
    • Objective criteria for the evaluation of clustering methods
    • Rand, W. Objective criteria for the evaluation of clustering methods J. Amer. Statist. Assoc. 1971, 66, 846-850
    • (1971) J. Amer. Statist. Assoc. , vol.66 , pp. 846-850
    • Rand, W.1
  • 22
    • 37049239596 scopus 로고
    • A computer program for classifying plants
    • Rogers, D. J.; Tanimoto, T. T. A computer program for classifying plants Science 1960, 132, 1115-1118
    • (1960) Science , vol.132 , pp. 1115-1118
    • Rogers, D.J.1    Tanimoto, T.T.2
  • 23
    • 84980090975 scopus 로고
    • The distribution of the flora of the alpine zone
    • Jaccard, P. The distribution of the flora of the alpine zone New Phytol. 1912, 11, 37-50
    • (1912) New Phytol. , vol.11 , pp. 37-50
    • Jaccard, P.1
  • 24
    • 0242390943 scopus 로고
    • Some applications of the quadrat method
    • Gleason, H. A. Some applications of the quadrat method Bull. Torrey Botanical Club 1920, 47, 21-33
    • (1920) Bull. Torrey Botanical Club , vol.47 , pp. 21-33
    • Gleason, H.A.1
  • 25
    • 0000250265 scopus 로고
    • Measures of the amount of ecological association between species
    • Dice, L. R. Measures of the amount of ecological association between species Ecology 1945, 26, 297-302
    • (1945) Ecology , vol.26 , pp. 297-302
    • Dice, L.R.1
  • 26
    • 0002969802 scopus 로고
    • A method for establishing groups of equal amplitude in plant sociology based on similarity of species content
    • Sørenson, T. A method for establishing groups of equal amplitude in plant sociology based on similarity of species content Biologiske Skrifter 1948, 5, 1-34
    • (1948) Biologiske Skrifter , vol.5 , pp. 1-34
    • Sørenson, T.1
  • 27
    • 0010539950 scopus 로고
    • On habitat and association of species of Anopheline larvae in South.Eastern Madras
    • Russell, P. F.; Rao, T. R. On habitat and association of species of Anopheline larvae in South.Eastern Madras J. Malaria Inst. India 1940, 3, 153-178
    • (1940) J. Malaria Inst. India , vol.3 , pp. 153-178
    • Russell, P.F.1    Rao, T.R.2
  • 28
    • 0006040005 scopus 로고
    • On the local distribution of certain Illinois fishes: An essay in statistical ecology
    • Forbes, S. A. On the local distribution of certain Illinois fishes: An essay in statistical ecology Bull. Illinois State Lab. Nat. History 1907, 7, 273-303
    • (1907) Bull. Illinois State Lab. Nat. History , vol.7 , pp. 273-303
    • Forbes, S.A.1
  • 29
    • 0001812683 scopus 로고
    • Mammals and the nature of continents
    • Simpson, G. G. Mammals and the nature of continents Am. J. Sci. 1943, 241, 1-31
    • (1943) Am. J. Sci. , vol.241 , pp. 1-31
    • Simpson, G.G.1
  • 32
    • 85007711844 scopus 로고
    • Zoogeographic studies on the soleoid fishes found in Japan and its neighboring regions
    • Ochiai, A. Zoogeographic studies on the soleoid fishes found in Japan and its neighboring regions Bull. Jpn. Soc. Fish Sci. 1957, 22, 526-530
    • (1957) Bull. Jpn. Soc. Fish Sci. , vol.22 , pp. 526-530
    • Ochiai, A.1
  • 36
    • 0023486365 scopus 로고
    • Compositional dissimilarity as a robust measure of ecological distance
    • Faith, D. P.; Minchin, P. R.; Belcin, L. Compositional dissimilarity as a robust measure of ecological distance Plant Ecol. 1987, 69, 57-68
    • (1987) Plant Ecol. , vol.69 , pp. 57-68
    • Faith, D.P.1    Minchin, P.R.2    Belcin, L.3
  • 37
    • 0001774008 scopus 로고
    • An index of similarity and its applications to classificatory problems
    • In; Murphy, P. W. Butterworths: London (UK)
    • Mountford, M. D. An index of similarity and its applications to classificatory problems. In Progress in Soil Zoology; Murphy, P. W., Ed.; Butterworths: London (UK), 1962; pp 43-50.
    • (1962) Progress in Soil Zoology , pp. 43-50
    • Mountford, M.D.1
  • 38
    • 0006041829 scopus 로고
    • Marine ecology and the coefficient of association
    • Michael, E. L. Marine ecology and the coefficient of association J. Animal Ecol. 1920, 8, 54-59
    • (1920) J. Animal Ecol. , vol.8 , pp. 54-59
    • Michael, E.L.1
  • 39
    • 0013944694 scopus 로고
    • A proposed index for measuring agreement in test-retest studies
    • Rogot, E.; Goldberg, I. D. A proposed index for measuring agreement in test-retest studies J. Chronic Disease 1966, 19, 991-1006
    • (1966) J. Chronic Disease , vol.19 , pp. 991-1006
    • Rogot, E.1    Goldberg, I.D.2
  • 40
    • 0010092286 scopus 로고
    • Reliability scores that delude: An Alice in Wonderful trip through the misleading characteristics of interobserver agreement scores in interval coding
    • In; Ramp, E. Semb, G. Prentic-Hall: Englewood Cliffs, NJ.
    • Hawkins, R. P.; Dotson, V. A. Reliability scores that delude: An Alice in Wonderful trip through the misleading characteristics of interobserver agreement scores in interval coding. In Behavior Analysis: Areas of Research and Application; Ramp, E.; Semb, G., Eds.; Prentic-Hall: Englewood Cliffs, NJ, 1968.
    • (1968) Behavior Analysis: Areas of Research and Application
    • Hawkins, R.P.1    Dotson, V.A.2
  • 41
    • 0001218846 scopus 로고
    • On the association of attributes in statistics
    • Yule, G. U. On the association of attributes in statistics Philos. Trans. R. Soc. A 1900, 75, 257-319
    • (1900) Philos. Trans. R. Soc. A , vol.75 , pp. 257-319
    • Yule, G.U.1
  • 42
    • 0000721530 scopus 로고
    • On the methods of measuring association between two attributes
    • Yule, G. U. On the methods of measuring association between two attributes J. R. Stat. Soc. 1912, 75, 579-642
    • (1912) J. R. Stat. Soc. , vol.75 , pp. 579-642
    • Yule, G.U.1
  • 43
    • 0000384188 scopus 로고
    • The measurement of interspecific association
    • Cole, L. C. The measurement of interspecific association Ecology 1949, 30, 411-424
    • (1949) Ecology , vol.30 , pp. 411-424
    • Cole, L.C.1
  • 45
    • 34248978779 scopus 로고
    • Measures of association for cross classifications
    • Goodman, L. A.; Kruskal, W. H. Measures of association for cross classifications J. Amer. Stat. Assoc. 1954, 49, 732-764
    • (1954) J. Amer. Stat. Assoc. , vol.49 , pp. 732-764
    • Goodman, L.A.1    Kruskal, W.H.2
  • 46
    • 0000220605 scopus 로고
    • On theories of association
    • Pearson, K.; Heron, D. On theories of association Biometrika 1913, 9, 159-315
    • (1913) Biometrika , vol.9 , pp. 159-315
    • Pearson, K.1    Heron, D.2
  • 47
    • 1842641692 scopus 로고
    • A method for comparing two hierarchical clusterings: Comment
    • Wallace, D. L. A method for comparing two hierarchical clusterings: Comment J. Am. Stat. Assoc. 1983, 78, 569-576
    • (1983) J. Am. Stat. Assoc. , vol.78 , pp. 569-576
    • Wallace, D.L.1
  • 48
    • 0013357313 scopus 로고
    • Nonparametric unfolding models for dichotomous data
    • Post, W. J.; Snijders, T. A. B. Nonparametric unfolding models for dichotomous data Methodika 1993, 7, 130-156
    • (1993) Methodika , vol.7 , pp. 130-156
    • Post, W.J.1    Snijders, T.A.B.2
  • 49
    • 0003367447 scopus 로고
    • Molluscan assemblages from the marine middle Miocene of South Jutland and their environments
    • Sorgenfrei, T. Molluscan assemblages from the marine middle Miocene of South Jutland and their environments Danmark Geologiske Undersøgelse. Serie 2 1959, 79, 403-408
    • (1959) Danmark Geologiske Undersøgelse. Serie 2 , vol.79 , pp. 403-408
    • Sorgenfrei, T.1
  • 50
    • 84973587732 scopus 로고
    • A coefficient of agreement for nominal scales
    • Cohen, J. A coefficient of agreement for nominal scales Educ. Psychol. Measurements 1960, 20, 37-46
    • (1960) Educ. Psychol. Measurements , vol.20 , pp. 37-46
    • Cohen, J.1
  • 51
    • 0001100430 scopus 로고
    • The numerical measure of the success of predictions
    • Peirce, C. S. The numerical measure of the success of predictions Science 1884, 4, 453-454
    • (1884) Science , vol.4 , pp. 453-454
    • Peirce, C.S.1
  • 52
    • 0014279913 scopus 로고
    • Deriving coefficients of reliability and agreement for ratings
    • Maxwell, A. E.; Pilliner, A. E. G. Deriving coefficients of reliability and agreement for ratings Brit. J. Math. Stat. Psychol. 1968, 21, 105-116
    • (1968) Brit. J. Math. Stat. Psychol. , vol.21 , pp. 105-116
    • Maxwell, A.E.1    Pilliner, A.E.G.2
  • 53
    • 84987306092 scopus 로고
    • A method for combining occurrence and nonoccurrence agreement scores
    • Harris, F. C.; Lahey, B. B. A method for combining occurrence and nonoccurrence agreement scores J. Appl. Behav. Anal. 1978, 11, 523-527
    • (1978) J. Appl. Behav. Anal. , vol.11 , pp. 523-527
    • Harris, F.C.1    Lahey, B.B.2
  • 55
    • 0017712746 scopus 로고
    • Evaluation of some coefficients for use in numerical taxonomy of microorganisms
    • Austin, B.; Colwell, R. R. Evaluation of Some Coefficients for Use in Numerical Taxonomy of Microorganisms Int. J. Syst. Bacteriol. 1977, 27, 204-210 (Pubitemid 8195098)
    • (1977) International Journal of Systematic Bacteriology , vol.27 , Issue.3 , pp. 204-210
    • Austin, B.1    Colwell, R.R.2
  • 56
    • 0041510433 scopus 로고
    • Merkmalsbestand und Verwandtschaftsbezienhungen der Farinose. Ein Betrag zum System der Monokotyledonen
    • Hamann, U. Merkmalsbestand und Verwandtschaftsbezienhungen der Farinose. Ein Betrag zum System der Monokotyledonen Willdenowia 1961, 2, 639-768
    • (1961) Willdenowia , vol.2 , pp. 639-768
    • Hamann, U.1
  • 58
    • 85004846287 scopus 로고
    • Nominal scale response agreement as a generalized correlation
    • Hubert, L. J. Nominal scale response agreement as a generalized correlation Brit. J. Math. Stat. Psych. 1977, 30, 98-103
    • (1977) Brit. J. Math. Stat. Psych. , vol.30 , pp. 98-103
    • Hubert, L.J.1
  • 59
    • 33750730174 scopus 로고
    • The determination and analysis of plankton communities
    • Special No., Indonesia
    • McConnaughey, B. H. The determination and analysis of plankton communities Mar. Res. 1964, Special No., Indonesia) 1-40
    • (1964) Mar. Res. , pp. 1-40
    • McConnaughey, B.H.1
  • 60
    • 33747044600 scopus 로고
    • Metric and Euclidean properties of dis-similarity coefficients
    • Gower, J. C.; Legendre, P. Metric and Euclidean properties of dis-similarity coefficients J. Classification 1986, 3, 5-48
    • (1986) J. Classification , vol.3 , pp. 5-48
    • Gower, J.C.1    Legendre, P.2
  • 61
    • 0014129195 scopus 로고
    • Hierarchical clustering schemes
    • Johnson, S. C. Hierarchical clustering schemes Psychometrika 1967, 32, 241-254
    • (1967) Psychometrika , vol.32 , pp. 241-254
    • Johnson, S.C.1
  • 62
    • 33748063869 scopus 로고
    • Reliability of content analysis:The case of nominal scale coding
    • Scott, W. A. Reliability of content analysis:The case of nominal scale coding Public Opin. Q. 1955, 19, 321-325
    • (1955) Public Opin. Q. , vol.19 , pp. 321-325
    • Scott, W.A.1
  • 63
    • 0142082987 scopus 로고
    • On the use of ordination models in phytosociology
    • van der Maarel, E. On the use of ordination models in phytosociology Vegetatio 1969, 19, 21-46
    • (1969) Vegetatio , vol.19 , pp. 21-46
    • Van Der Maarel, E.1
  • 65
    • 65349136650 scopus 로고    scopus 로고
    • Maximum Unbiased Validation (MUV) data sets for virtual screening based on PubChem bioactivity data
    • Rohrer, S. G.; Baumann, K. Maximum Unbiased Validation (MUV) data sets for virtual screening based on PubChem bioactivity data J. Chem. Inf. Model. 2009, 49, 169-184
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 169-184
    • Rohrer, S.G.1    Baumann, K.2
  • 66
    • 77952772341 scopus 로고    scopus 로고
    • Extended-connectivity fingerprints
    • Rogers, D.; Hahn, M. Extended-connectivity fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 742-754
    • Rogers, D.1    Hahn, M.2
  • 68
    • 84870964506 scopus 로고    scopus 로고
    • ver. 7.1. StatSoft, Padova, Italy.
    • STATISTICA, ver. 7.1. StatSoft, Padova, Italy.
    • STATISTICA
  • 70
    • 2942710342 scopus 로고    scopus 로고
    • Application of the concept of partial order on comparative evaluation of environmental chemicals
    • DOI 10.1002/(SICI)1521-401X(199905)27:3<170::AID-AHEH170>3.0.CO;2-9
    • Brüggemann, R.; Bücherl, C.; Pudenz, S.; Steinberg, E. W. Application of the Concept of Partial Order on Comparative Evaluation of Environmental Chemicals Acta Hydrochim. Hydrobiol. 1999, 27, 170-178 (Pubitemid 29419296)
    • (1999) Acta Hydrochimica et Hydrobiologica , vol.27 , Issue.3 , pp. 170-178
    • Bruggemann, R.1    Bucherl, C.2    Pudenz, S.3    Steinberg, C.E.W.4
  • 71
    • 84870973244 scopus 로고    scopus 로고
    • DART software (Decision Analysis by Ranking Techniques)
    • DART software (Decision Analysis by Ranking Techniques), 2007; www.talete.mi.it.
    • (2007)
  • 72
    • 0037835585 scopus 로고    scopus 로고
    • Analysis and Display of the Size Dependence of Chemical Similarity Coefficients
    • Holliday, J. D.; Salim, N.; Whittle, M.; Willett, P. Analysis and Display of the Size Dependence of Chemical Similarity Coefficients J. Chem. Inf. Comput. Sci. 2003, 43, 819-828
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 819-828
    • Holliday, J.D.1    Salim, N.2    Whittle, M.3    Willett, P.4
  • 73
    • 85032415954 scopus 로고    scopus 로고
    • ATDM Algorithm. In, version 16.0; Semeion Software no. 51, Rome, Italy, 2008-2012.
    • Buscema, M. ATDM Algorithm. In Modular Auto Associative ANNs, version 16.0; Semeion Software no. 51, Rome, Italy, 2008-2012; www.semeion.it.
    • Modular Auto Associative ANNs
    • Buscema, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.