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Volumn 47, Issue 5, 2007, Pages 1727-1733

Development of a spectral clustering method for the analysis of molecular data sets

Author keywords

[No Author keywords available]

Indexed keywords

DATA REDUCTION; DATA STRUCTURES; SPECTRUM ANALYSIS;

EID: 35248839332     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600565r     Document Type: Article
Times cited : (15)

References (29)
  • 1
    • 33645265985 scopus 로고    scopus 로고
    • Clustering Methods and Their Uses in Computational Chemistry
    • Downs, G. M; Barnard J. M. Clustering Methods and Their Uses in Computational Chemistry, Rev. Comput. Chem. 2002, 18, 1-40.
    • (2002) Rev. Comput. Chem , vol.18 , pp. 1-40
    • Downs, G.M.1    Barnard, J.M.2
  • 3
    • 0015680655 scopus 로고
    • Clustering Using a Similarity Measure Based on Shared Near Neighbours
    • Jarvis, R. A.; Patrick, E. A. Clustering Using a Similarity Measure Based on Shared Near Neighbours. IEEE Trans. Comput. 1973, C-22, 1025-1034.
    • (1973) IEEE Trans. Comput , vol.C-22 , pp. 1025-1034
    • Jarvis, R.A.1    Patrick, E.A.2
  • 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 Binding
    • Brown, R. D.; Martin, Y. C. The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding. 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
    • 84944178665 scopus 로고
    • Hierarchical grouping to optimize an objective function
    • Ward, J. H. Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 1963, 55, 236-244.
    • (1963) J. Am. Stat. Assoc , vol.55 , pp. 236-244
    • Ward, J.H.1
  • 8
    • 18244365837 scopus 로고    scopus 로고
    • Wilkens, S. J.; Janes, J.; Su, A. I. HierS: Heirarchical Scaffold Clustering Using Topological Chemical Graphs. J. Med. Chem. 2005, 48, 3182-3193.
    • Wilkens, S. J.; Janes, J.; Su, A. I. HierS: Heirarchical Scaffold Clustering Using Topological Chemical Graphs. J. Med. Chem. 2005, 48, 3182-3193.
  • 9
    • 21244496075 scopus 로고    scopus 로고
    • Stahl, M.; Mauser, H.; Tsui, M.; Taylor, N. R. A Robust Clustering Method for Chemical Structures. J. Med. Chem. 2005, 48, 4358-4366.
    • Stahl, M.; Mauser, H.; Tsui, M.; Taylor, N. R. A Robust Clustering Method for Chemical Structures. J. Med. Chem. 2005, 48, 4358-4366.
  • 10
    • 20444410051 scopus 로고    scopus 로고
    • Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods
    • Stahl, M.; Mauser, H. Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods. J. Chem. Inf. Model. 2005, 45, 542-548.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 542-548
    • Stahl, M.1    Mauser, H.2
  • 11
    • 23844460001 scopus 로고    scopus 로고
    • Böcker, A.; Derksen, S.; Schmidt, E.; Teckentrup, A.; Schneider, G. A Hierarchical Clustering Approach for Large Compound Libraries. J. Chem. Inf. Model. 2005, 45, 807-815.
    • Böcker, A.; Derksen, S.; Schmidt, E.; Teckentrup, A.; Schneider, G. A Hierarchical Clustering Approach for Large Compound Libraries. J. Chem. Inf. Model. 2005, 45, 807-815.
  • 12
    • 33845810666 scopus 로고    scopus 로고
    • Böcker, A.; Schneider, G.; Teckentrup, A. NIPALSTREE: A New Hierarchical Clustering Approach for Large Compound Libraries and Its Application to Virtual Screening. J. Chem. Inf. Model. 2006, 46, 2220-2229.
    • Böcker, A.; Schneider, G.; Teckentrup, A. NIPALSTREE: A New Hierarchical Clustering Approach for Large Compound Libraries and Its Application to Virtual Screening. J. Chem. Inf. Model. 2006, 46, 2220-2229.
  • 13
    • 33750341686 scopus 로고    scopus 로고
    • Li, W. A Fast Clustering Algorithm for Analyzing Highly Similar Compounds of Very Large Libraries. J. Chem. Inf. Model. 2006, 46, 1919-1923.
    • Li, W. A Fast Clustering Algorithm for Analyzing Highly Similar Compounds of Very Large Libraries. J. Chem. Inf. Model. 2006, 46, 1919-1923.
  • 14
    • 33845867934 scopus 로고    scopus 로고
    • Engels, M. F.; Gibbs, A. C.; Jaeger, E. P.; Verbinnen, D.; Lobanov, V. S.; Agrafiotis, D. K. A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries and Its Application to a Recent Acquisition. J. Chem. Inf. Model. 2006, 46, 2651-2660.
    • Engels, M. F.; Gibbs, A. C.; Jaeger, E. P.; Verbinnen, D.; Lobanov, V. S.; Agrafiotis, D. K. A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries and Its Application to a Recent Acquisition. J. Chem. Inf. Model. 2006, 46, 2651-2660.
  • 15
    • 12244275244 scopus 로고    scopus 로고
    • Biological spectra analysis: Linking biological activity profiles to molecular structure
    • Fliri, A. F.; Loging, W. T.; Thadeio, P. F.; Volkmann, R. A. Biological spectra analysis: Linking biological activity profiles to molecular structure. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 261-266.
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 261-266
    • Fliri, A.F.1    Loging, W.T.2    Thadeio, P.F.3    Volkmann, R.A.4
  • 16
    • 32344440237 scopus 로고    scopus 로고
    • Analysis of drug-induced effect patterns to link structure and side effects of medicines
    • Fliri, A. F.; Loging, W. T.; Thadeio, P. F.; Volkmann, R. A. Analysis of drug-induced effect patterns to link structure and side effects of medicines. Nat. Chem. Biol. 2005, 1, 389-397.
    • (2005) Nat. Chem. Biol , vol.1 , pp. 389-397
    • Fliri, A.F.1    Loging, W.T.2    Thadeio, P.F.3    Volkmann, R.A.4
  • 17
    • 0000353230 scopus 로고    scopus 로고
    • The Characterisation of Chemical Structures using Molecular Properties. A Survey
    • Livingstone, D. J. The Characterisation of Chemical Structures using Molecular Properties. A Survey. J. Chem. Inf. Comput. Sci. 2000, 40, 195-209.
    • (2000) J. Chem. Inf. Comput. Sci , vol.40 , pp. 195-209
    • Livingstone, D.J.1
  • 18
    • 0001202274 scopus 로고    scopus 로고
    • Explicit Calculation of 3D Molecular Similarity
    • Good, A. C; Richards, W. G. Explicit Calculation of 3D Molecular Similarity. Perspect. Drug Discovery Des. 1998, 9-11, 321-338.
    • (1998) Perspect. Drug Discovery Des , vol.9-11 , pp. 321-338
    • Good, A.C.1    Richards, W.G.2
  • 24
    • 0032121920 scopus 로고    scopus 로고
    • Quantitative Measures of Change Based on Feature Organization: Eigenvalues and Eigenvectors
    • Sarkar, S.; Boyer, K. L. Quantitative Measures of Change Based on Feature Organization: Eigenvalues and Eigenvectors. Comput. Vision Image Understanding 1998, 71, 110-136.
    • (1998) Comput. Vision Image Understanding , vol.71 , pp. 110-136
    • Sarkar, S.1    Boyer, K.L.2
  • 26
    • 35248872476 scopus 로고    scopus 로고
    • Eigenvectors that yield discriminating clusters are positive, meaning all elements of the eigenvector share the same sign, but as Sarkar and Boyer have demonstrated this condition can be partially relaxed, and eigenvectors with dominant positive components also provide discriminating clusters. The condition may be completely relaxed if overlap is acceptable between the resultant clusters
    • Eigenvectors that yield discriminating clusters are positive, meaning all elements of the eigenvector share the same sign, but as Sarkar and Boyer have demonstrated this condition can be partially relaxed, and eigenvectors with dominant positive components also provide discriminating clusters. The condition may be completely relaxed if overlap is acceptable between the resultant clusters.
  • 27
    • 35248818270 scopus 로고    scopus 로고
    • cheminformatics.org. http://www.cheminformatics.orgy (accessed Dec 21, 2006).
    • cheminformatics.org. http://www.cheminformatics.orgy (accessed Dec 21, 2006).
  • 28
    • 35248821293 scopus 로고    scopus 로고
    • SYBYL, version 7.2; Tripos: St. Louis, MO, 2006
    • SYBYL, version 7.2; Tripos: St. Louis, MO, 2006.
  • 29
    • 35248882943 scopus 로고    scopus 로고
    • MOE, version 2006.08; Chemical Computing Group: Montreal, Quebec, 2006
    • MOE, version 2006.08; Chemical Computing Group: Montreal, Quebec, 2006.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.