메뉴 건너뛰기




Volumn 51, Issue 7, 2011, Pages 1521-1527

GPU accelerated chemical similarity calculation for compound library comparison

Author keywords

[No Author keywords available]

Indexed keywords

CALCULATIONS; DIGITAL LIBRARIES; GRAPHICS PROCESSING UNIT; NEAREST NEIGHBOR SEARCH; PARALLEL PROGRAMMING; PROGRAM PROCESSORS;

EID: 79960741112     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci1004948     Document Type: Article
Times cited : (79)

References (25)
  • 1
    • 33745859416 scopus 로고    scopus 로고
    • Methods for mining HTS data
    • DOI 10.1016/j.drudis.2006.06.006, PII S1359644606002133
    • Harper, G.; Pickett, S. D. Methods for mining HTS data Drug Discovery Today 2006, 11 (15-16) 694-9 (Pubitemid 44038624)
    • (2006) Drug Discovery Today , vol.11 , Issue.15-16 , pp. 694-699
    • Harper, G.1    Pickett, S.D.2
  • 2
    • 1042265247 scopus 로고    scopus 로고
    • Approaches to Measure Chemical Similarity-a Review
    • Nikolova, N.; Jaworska, J. Approaches to Measure Chemical Similarity-a Review QSAR Comb. Sci. 2003, 22 (9-10) 1006-1026
    • (2003) QSAR Comb. Sci. , vol.22 , Issue.9-10 , pp. 1006-1026
    • Nikolova, N.1    Jaworska, J.2
  • 5
    • 0029382598 scopus 로고
    • Characterising the geometric diversity of functional groups in chemical databases
    • Boyd, S. M.; Beverley, M.; Norskov, L.; Hubbard, R. E. Characterising the geometric diversity of functional groups in chemical databases J. Comput.-Aided Mol. Des. 1995, 9 (5) 417-424
    • (1995) J. Comput.-Aided Mol. Des. , vol.9 , Issue.5 , pp. 417-424
    • Boyd, S.M.1    Beverley, M.2    Norskov, L.3    Hubbard, R.E.4
  • 6
    • 0028953765 scopus 로고
    • Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery
    • Martin, E. J.; Blaney, J. M.; Siani, M. A.; Spellmeyer, D. C.; Wong, A. K.; Moos, W. H. Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery J. Med. Chem. 1995, 38 (9) 1431-1436
    • (1995) J. Med. Chem. , vol.38 , Issue.9 , pp. 1431-1436
    • Martin, E.J.1    Blaney, J.M.2    Siani, M.A.3    Spellmeyer, D.C.4    Wong, A.K.5    Moos, W.H.6
  • 7
    • 0030191461 scopus 로고    scopus 로고
    • Molecular diversity in chemical databases: Comparison of medicinal chemistry knowledge bases and databases of commercially available compounds
    • Cummins, D. J.; Andrews, C. W.; Bentley, J. A.; Cory, M. Molecular Diversity in Chemical Databases: Comparison of Medicinal Chemistry Knowledge Bases and Databases of Commercially Available Compounds J. Chem. Inf. Comput. Sci. 1996, 36 (4) 750-763 (Pubitemid 126581727)
    • (1996) Journal of Chemical Information and Computer Sciences , vol.36 , Issue.4 , pp. 750-763
    • Cummins, D.J.1    Andrews, C.W.2    Bentley, J.A.3    Cory, M.4
  • 8
    • 66149148225 scopus 로고    scopus 로고
    • Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository
    • Singh, N.; Guha, R.; Giulianotti, M. A.; Pinilla, C.; Houghten, R. A.; Medina-Franco, J. L. Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository J. Chem. Inf. Comput. Sci. 2009, 49 (4) 1010-1024
    • (2009) J. Chem. Inf. Comput. Sci. , vol.49 , Issue.4 , pp. 1010-1024
    • Singh, N.1    Guha, R.2    Giulianotti, M.A.3    Pinilla, C.4    Houghten, R.A.5    Medina-Franco, J.L.6
  • 9
    • 67650650984 scopus 로고    scopus 로고
    • Construction of a Bicyclic β-Benzyloxy and β-Hydroxy Amide Library through a Multicomponent Cyclization Reaction
    • Zhang, L.; Xiao, Q.; Ma, C.; Xie, X.-Q.; Floreancig, P. E. Construction of a Bicyclic β-Benzyloxy and β-Hydroxy Amide Library through a Multicomponent Cyclization Reaction J. Comb. Chem. 2009, 11 (4) 640-644
    • (2009) J. Comb. Chem. , vol.11 , Issue.4 , pp. 640-644
    • Zhang, L.1    Xiao, Q.2    Ma, C.3    Xie, X.-Q.4    Floreancig, P.E.5
  • 10
    • 0036835460 scopus 로고    scopus 로고
    • Integration of virtual and high-throughput screening
    • DOI 10.1038/nrd941
    • Bajorath, J. Integration of virtual and high-throughput screening Nat. Rev. Drug Discovery 2002, 1 (11) 882-94 (Pubitemid 37361583)
    • (2002) Nature Reviews Drug Discovery , vol.1 , Issue.11 , pp. 882-894
    • Bajorath, J.1
  • 11
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity?
    • DOI 10.1021/jm020155c
    • Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity? J. Med. Chem. 2002, 45 (19) 4350-8 (Pubitemid 35025581)
    • (2002) Journal of Medicinal Chemistry , vol.45 , Issue.19 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 12
    • 42149150001 scopus 로고    scopus 로고
    • Data mining a small molecule drug screening representative subset from NIH PubChem
    • DOI 10.1021/ci700193u
    • Xie, X.-Q.; Chen, J.-Z. Data Mining a Small Molecule Drug Screening Representative Subset from NIH PubChem J. Chem. Inf. Model. 2008, 48 (3) 465-475 (Pubitemid 351535416)
    • (2008) Journal of Chemical Information and Modeling , vol.48 , Issue.3 , pp. 465-475
    • Xie, X.-Q.1    Chen, J.-Z.2
  • 13
    • 79960701956 scopus 로고    scopus 로고
    • SYBYL 8.0; Tripos International: 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA
    • SYBYL 8.0; Tripos International: 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA, 2008.
    • (2008)
  • 14
    • 79960702905 scopus 로고    scopus 로고
    • Tripos Bookshelf 8.0; Tripos International: 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA
    • Tripos Bookshelf 8.0; Tripos International: 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA, 2007.
    • (2007)
  • 15
    • 65249163404 scopus 로고    scopus 로고
    • Searching for Target-Selective Compounds Using Different Combinations of Multiclass Support Vector Machine Ranking Methods, Kernel Functions, and Fingerprint Descriptors
    • Wassermann, A. M.; Geppert, H.; Bajorath, J. Searching for Target-Selective Compounds Using Different Combinations of Multiclass Support Vector Machine Ranking Methods, Kernel Functions, and Fingerprint Descriptors J. Chem. Inf. Model. 2009, 49 (3) 582-592
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.3 , pp. 582-592
    • Wassermann, A.M.1    Geppert, H.2    Bajorath, J.3
  • 16
    • 0000892020 scopus 로고    scopus 로고
    • Clustering of large databases of compounds: Using the MDL 'keys' as structural descriptors
    • McGregor, M. J.; Pallai, P. V. Clustering of Large Databases of Compounds: Using the MDL "Keys" as Structural Descriptors J. Chem. Inf. Comput. Sci. 1997, 37, 443-448 (Pubitemid 127603548)
    • (1997) Journal of Chemical Information and Computer Sciences , vol.37 , Issue.3 , pp. 443-448
    • McGregor, M.J.1    Pallai, P.V.2
  • 17
    • 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 (4) 747-750
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , Issue.4 , pp. 747-750
    • Butina, D.1
  • 18
    • 67849104638 scopus 로고    scopus 로고
    • PubChem: A public information system for analyzing bioactivities of small molecules
    • Wang, Y.; Xiao, J.; Suzek, T. O.; Zhang, J.; Wang, J.; Bryant, S. H. PubChem: a public information system for analyzing bioactivities of small molecules Nucleic Acids Res. 2009, 37 (Web Server issue) W623-33
    • (2009) Nucleic Acids Res. , vol.37 , Issue.WEB SERVER ISSUE , pp. 623-633
    • Wang, Y.1    Xiao, J.2    Suzek, T.O.3    Zhang, J.4    Wang, J.5    Bryant, S.H.6
  • 19
    • 78649386109 scopus 로고    scopus 로고
    • Exploiting PubChem for virtual screening
    • Xie, X.-Q. Exploiting PubChem for virtual screening Expert Opin. Drug Discovery 2010, 5 (12) 1205-1220
    • (2010) Expert Opin. Drug Discovery , vol.5 , Issue.12 , pp. 1205-1220
    • Xie, X.-Q.1
  • 20
    • 77955732124 scopus 로고    scopus 로고
    • Quantum Chemistry on Graphics Processing Units
    • In, Ralph, A. W., Ed.; Elsevier:
    • Götz, A. W.; Wölfle, T.; Walker, R. C., Quantum Chemistry on Graphics Processing Units. In Annu. Rep. Comput. Chem., Ralph, A. W., Ed.; Elsevier: 2010; Vol. 6, pp 21-35.
    • (2010) Annu. Rep. Comput. Chem. , vol.6 , pp. 21-35
    • Götz, A.W.1    Wölfle, T.2    Walker, R.C.3
  • 21
    • 77955764321 scopus 로고    scopus 로고
    • Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units
    • In, Ralph, A. W., Ed.; Elsevier:
    • Xu, D.; Williamson, M. J.; Walker, R. C., Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units. In Annu. Rep. Comput. Chem., Ralph, A. W., Ed.; Elsevier: 2010; Vol. 6, pp 2-19.
    • (2010) Annu. Rep. Comput. Chem. , vol.6 , pp. 2-19
    • Xu, D.1    Williamson, M.J.2    Walker, R.C.3
  • 22
    • 77952004390 scopus 로고    scopus 로고
    • SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs
    • Haque, I. S.; Pande, V. S.; Walters, W. P. SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs J. Chem. Inf. Model. 2010, 50 (4) 560-564
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.4 , pp. 560-564
    • Haque, I.S.1    Pande, V.S.2    Walters, W.P.3
  • 23
    • 73349088447 scopus 로고    scopus 로고
    • GPU accelerated support vector machines for mining high-throughput screening data
    • Liao, Q.; Wang, J.; Webster, Y.; Watson, I. A. GPU accelerated support vector machines for mining high-throughput screening data J. Chem. Inf. Model. 2009, 49 (12) 2718-25
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.12 , pp. 2718-2725
    • Liao, Q.1    Wang, J.2    Webster, Y.3    Watson, I.A.4
  • 24
    • 68849090741 scopus 로고    scopus 로고
    • Evaluating the Jaccard-Tanimoto Index on Multi-core Architectures
    • In; Allen, G.; Nabrzyski, J.; Seidel, E.; van Albada, G.; Dongarra, J.; Sloot, P., Eds.; Springer: Berlin/Heidelberg:
    • Sachdeva, V.; Freimuth, D.; Mueller, C., Evaluating the Jaccard-Tanimoto Index on Multi-core Architectures. In Computational Science-ICCS 2009; Allen, G.; Nabrzyski, J.; Seidel, E.; van Albada, G.; Dongarra, J.; Sloot, P., Eds.; Springer: Berlin/Heidelberg: 2009; Vol. 5544, pp 944-953.
    • (2009) Computational Science-ICCS 2009 , vol.5544 , pp. 944-953
    • Sachdeva, V.1    Freimuth, D.2    Mueller, C.3
  • 25
    • 79960719907 scopus 로고    scopus 로고
    • NVIDIA CUDA ZONE. (accessed Dec 10)
    • NVIDIA CUDA ZONE. http://www.nvidia.com/object/cuda-home-new.html (accessed Dec 10, 2010).
    • (2010)


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.