메뉴 건너뛰기




Volumn 55, Issue 1, 2015, Pages 39-53

Development of a novel fingerprint for chemical reactions and its application to large-scale reaction classification and similarity

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REACTIONS; CLUSTER ANALYSIS; EXPERT SYSTEMS; MACHINE LEARNING; PHYSICOCHEMICAL PROPERTIES; PREDICTIVE ANALYTICS;

EID: 84921799235     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci5006614     Document Type: Article
Times cited : (144)

References (40)
  • 1
    • 84955734139 scopus 로고    scopus 로고
    • Reaction Classification and Knowledge Acquisition
    • Gasteiger, J., Ed.; Wiley-VCH Verlag: Weinheim, Germany
    • Chen, L. Reaction Classification and Knowledge Acquisition. In Handbook of Chemoinformatics; Gasteiger, J., Ed.; Wiley-VCH Verlag: Weinheim, Germany, 2003; pp 348-390.
    • (2003) Handbook of Chemoinformatics , pp. 348-390
    • Chen, L.1
  • 2
    • 84902817544 scopus 로고    scopus 로고
    • Review of Chemical Reaction Database Systems, Computer-Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility
    • Warr, W. A.; Short, A. Review of Chemical Reaction Database Systems, Computer-Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility. Mol. Informatics 2014, 33 (6-7), 469-476.
    • (2014) Mol. Informatics , vol.33 , Issue.6-7 , pp. 469-476
    • Warr, W.A.1    Short, A.2
  • 4
    • 84921729052 scopus 로고    scopus 로고
    • (accessed January 2015)
    • RSC's RXNO Ontology: http://www.rsc.org/ontologies/RXNO/index.asp (accessed January 2015).
    • RSC's RXNO Ontology
  • 8
    • 0000274551 scopus 로고
    • Building and refining a knowledge base for synthetic organic chemistry via the methodology of inductive and deductive machine learning
    • Gelernter, H.; Rose, J. R.; Chen, C. Building and refining a knowledge base for synthetic organic chemistry via the methodology of inductive and deductive machine learning. J. Chem. Inf. Comput. Sci. 1990, 30 (4), 492-504.
    • (1990) J. Chem. Inf. Comput. Sci. , vol.30 , Issue.4 , pp. 492-504
    • Gelernter, H.1    Rose, J.R.2    Chen, C.3
  • 9
    • 0030881321 scopus 로고    scopus 로고
    • Classification of organic reactions using similarity
    • Sello, G.; Termini, M. Classification of organic reactions using similarity. Tetrahedron 1997, 53 (41), 14085-14106.
    • (1997) Tetrahedron , vol.53 , Issue.41 , pp. 14085-14106
    • Sello, G.1    Termini, M.2
  • 10
    • 84888628910 scopus 로고    scopus 로고
    • Analysis of Reaction Information
    • Wiley-VCH Verlag: Weinheim, Germany
    • Grethe, G. Analysis of Reaction Information. In Handbook of Chemoinformatics; Wiley-VCH Verlag: Weinheim, Germany, 2003; pp 1407-1427.
    • (2003) Handbook of Chemoinformatics , pp. 1407-1427
    • Grethe, G.1
  • 11
    • 84864201010 scopus 로고    scopus 로고
    • Mining electronic laboratory notebooks: Analysis, retrosynthesis, and reaction based enumeration
    • Christ, C. D.; Zentgraf, M.; Kriegl, J. M. Mining electronic laboratory notebooks: analysis, retrosynthesis, and reaction based enumeration. J. Chem. Inf. Model. 2012, 52 (7), 1745-1756.
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.7 , pp. 1745-1756
    • Christ, C.D.1    Zentgraf, M.2    Kriegl, J.M.3
  • 12
    • 84921788030 scopus 로고    scopus 로고
    • (accessed October 17, 2014)
    • Daylight Reaction Fingerprint. http://www.daylight.com/dayhtml/doc/theory/theory.finger.html (accessed October 17, 2014).
    • Daylight Reaction Fingerprint
  • 13
    • 84905564623 scopus 로고    scopus 로고
    • Methods for Classifying and Searching Chemical Reactions
    • U.S. Patent
    • Broughton, H. B.; Hunt, P. A.; MacKey, M. D. Methods for Classifying and Searching Chemical Reactions. U.S. Patent 2003/0182094 A1, 2003.
    • (2003)
    • Broughton, H.B.1    Hunt, P.A.2    MacKey, M.D.3
  • 14
    • 47649092672 scopus 로고    scopus 로고
    • SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites
    • Ridder, L.; Wagener, M. SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites. ChemMed-Chem. 2008, 3, 821-832.
    • (2008) ChemMed-Chem. , vol.3 , pp. 821-832
    • Ridder, L.1    Wagener, M.2
  • 15
    • 66249098082 scopus 로고    scopus 로고
    • Knowledge-Based Approach to de NovoDesign Using Reaction Vectors
    • Patel, H.; Bodkin, M. J.; Chen, B.; Gillet, V. J. Knowledge-Based Approach to de NovoDesign Using Reaction Vectors. J. Chem. Inf. Model. 2009, 49, 1163-1184.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1163-1184
    • Patel, H.1    Bodkin, M.J.2    Chen, B.3    Gillet, V.J.4
  • 16
    • 33244456816 scopus 로고    scopus 로고
    • Molecular transformations as a way of finding and exploiting consistent local QSAR
    • Sheridan, R. P.; Hunt, P.; Culberson, J. C. Molecular transformations as a way of finding and exploiting consistent local QSAR. J. Chem. Inf. Model. 2006, 46, 180-192.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 180-192
    • Sheridan, R.P.1    Hunt, P.2    Culberson, J.C.3
  • 17
    • 54949108677 scopus 로고    scopus 로고
    • PubChem: Integrated Platform of Small Molecules and Biological Activities
    • American Chemical Society: Washington, DC
    • Bolton, E.; Wang, Y.; Thiessen, P. A.; Bryant, S. H. PubChem: Integrated Platform of Small Molecules and Biological Activities. In Annual Reports in Computational Chemistry; Vol. 4; American Chemical Society: Washington, DC, 2008.
    • (2008) Annual Reports in Computational Chemistry , vol.4
    • Bolton, E.1    Wang, Y.2    Thiessen, P.A.3    Bryant, S.H.4
  • 20
    • 0000777061 scopus 로고
    • CASREACT: More than a million reactions
    • Blake, J. E.; Dana, R. C. CASREACT: More than a million reactions. J. Chem. Inf. Comput. Sci. 1990, 30 (4), 394-399.
    • (1990) J. Chem. Inf. Comput. Sci. , vol.30 , Issue.4 , pp. 394-399
    • Blake, J.E.1    Dana, R.C.2
  • 21
    • 84921759589 scopus 로고    scopus 로고
    • (accessed October 17, 2014)
    • Reaxys Database. http://www.elsevier.com/online-tools/reaxys (accessed October 17, 2014).
    • Reaxys Database
  • 22
    • 84921723933 scopus 로고    scopus 로고
    • (accessed October 17, 2014)
    • SPRESI Database. http://infochem.de/products/databases/spresi.shtml (accessed October 17, 2014).
    • SPRESI Database
  • 24
    • 84921758440 scopus 로고    scopus 로고
    • (accessed October 17, 2014)
    • Webreactions Database. http://www.openmolecules.org/webreactions/index.html (accessed October 17, 2014).
    • Webreactions Database
  • 26
    • 84921763470 scopus 로고    scopus 로고
    • Patent Data: (accessed on October 17, 2014)
    • Patent Data: http://nextmovesoftware.com/blog/2014/02/27/ unleashing-over-a-million-reactions-into-the-wild/,https://bitbucket.org/dan2097/patent-reaction-extraction/downloads (accessed on October 17, 2014).
  • 27
    • 33745079610 scopus 로고    scopus 로고
    • Analysis of the Reactions Used for the Preparation of Drug Candidate Molecules
    • Carey, J. S.; Laffan, D.; Thomson, C.; Williams, M. T. Analysis of the Reactions Used for the Preparation of Drug Candidate Molecules. Org. Biomol. Chem. 2006, 4, 2337-2347.
    • (2006) Org. Biomol. Chem. , vol.4 , pp. 2337-2347
    • Carey, J.S.1    Laffan, D.2    Thomson, C.3    Williams, M.T.4
  • 28
    • 79957698619 scopus 로고    scopus 로고
    • The Medicinal Chemist's Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates
    • Roughley, S. D.; Jordan, A. M. The Medicinal Chemist's Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates. J. Med. Chem. 2011, 54 (10), 3451-3479.
    • (2011) J. Med. Chem. , vol.54 , Issue.10 , pp. 3451-3479
    • Roughley, S.D.1    Jordan, A.M.2
  • 29
    • 84921778553 scopus 로고    scopus 로고
    • (accessed October 17, 2014)
    • NextMove Software. www.nextmovesoftware.com (accessed October 17, 2014).
    • NextMove Software
  • 30
    • 84858909192 scopus 로고    scopus 로고
    • (accessed October 17, 2014)
    • Indigo Software. http://ggasoftware.com/opensource/indigo/ (accessed October 17, 2014).
    • Indigo Software
  • 33
    • 34247481878 scopus 로고    scopus 로고
    • IPython: A System for Interactive Scientific Computing
    • (accessed January 2015)
    • Pérez, F.; Granger, B. E. IPython: A System for Interactive Scientific Computing, Comp. Sci. Eng. 2007, 9 (3), 21-29. URL: http://ipython.org (accessed January 2015).
    • (2007) Comp. Sci. Eng. , vol.9 , Issue.3 , pp. 21-29
    • Pérez, F.1    Granger, B.E.2
  • 34
    • 0023965741 scopus 로고
    • SMILES, A Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules
    • Weininger, D. SMILES, A Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Model. 1988, 28 (1), 31-36.
    • (1988) J. Chem. Inf. Model. , vol.28 , Issue.1 , pp. 31-36
    • Weininger, D.1
  • 35
    • 33845379303 scopus 로고
    • Atom Pairs As Molecular Features in Structure-Activity Studies: Definition and Applications
    • Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom Pairs As Molecular Features in Structure-Activity Studies: Definition and Applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
    • (1985) J. Chem. Inf. Comput. Sci. , vol.25 , pp. 64-73
    • Carhart, R.E.1    Smith, D.H.2    Venkataraghavan, R.3
  • 36
    • 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
  • 37
    • 0003076470 scopus 로고
    • Topological Torsion: A New Molecular Descriptor for SAR Applications. Comparison with Other Descriptors
    • Nilakantan, R.; Baumann, N.; Dixon, J. S.; Venkataraghavan, R. Topological Torsion: 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    Baumann, N.2    Dixon, J.S.3    Venkataraghavan, R.4
  • 38
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman, L. Random Forests. Machine Learning 2001, 45 (1), 5-32.
    • (2001) Machine Learning , vol.45 , Issue.1 , pp. 5-32
    • Breiman, L.1
  • 39
    • 0032671931 scopus 로고    scopus 로고
    • Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets
    • Butina, D. Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets. J. Chem. Inf. Comput. Sci. 1999, 39, 747-750.
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 747-750
    • Butina, D.1
  • 40
    • 0000250265 scopus 로고
    • Measures of the Amount of Ecologic Association Between Species
    • Dice, L. R. Measures of the Amount of Ecologic Association Between Species. Ecology 1945, 26, 297-302.
    • (1945) Ecology , vol.26 , pp. 297-302
    • Dice, L.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.