메뉴 건너뛰기




Volumn 50, Issue 8, 2010, Pages 1418-1431

Predicting polypharmacology by binding site similarity: From kinases to the protein universe

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; DRUG INTERACTIONS; FORECASTING;

EID: 77956040404     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci1001263     Document Type: Article
Times cited : (98)

References (38)
  • 1
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • Hopkins, A. L. Network pharmacology: the next paradigm in drug discovery Nat. Chem. Biol. 2008, 4, 682-690
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 2
    • 0033816156 scopus 로고    scopus 로고
    • Abl protein-tyrosine kinase inhibitor STI571 inhibits in vitro signal transduction mediated by c-kit and platelet-derived growth factor receptors
    • Buchdunger, E.; Cioffi, C. L.; Law, N.; Stover, D.; Ohno-Jones, S.; Druker, B. J.; Lydon, N. B. Abl protein-tyrosine kinase inhibitor STI571 inhibits in vitro signal transduction mediated by c-kit and platelet-derived growth factor receptors J. Pharmacol. Exp. Ther. 2000, 295, 139-145
    • (2000) J. Pharmacol. Exp. Ther. , vol.295 , pp. 139-145
    • Buchdunger, E.1    Cioffi, C.L.2    Law, N.3    Stover, D.4    Ohno-Jones, S.5    Druker, B.J.6    Lydon, N.B.7
  • 4
    • 76649139794 scopus 로고    scopus 로고
    • Computational approaches to identifying and characterizing protein binding sites for ligand design
    • Henrich, S.; Salo-Ahen, O. M. H.; Huang, B.; Rippmann, F. F.; Cruciani, G.; Wade, R. C. Computational approaches to identifying and characterizing protein binding sites for ligand design J. Mol. Recog. 2010, 23, 209-219
    • (2010) J. Mol. Recog. , vol.23 , pp. 209-219
    • Henrich, S.1    Salo-Ahen, O.M.H.2    Huang, B.3    Rippmann, F.F.4    Cruciani, G.5    Wade, R.C.6
  • 6
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favourable binding sites on biologically important macromolecules
    • Goodford, P. J. A computational procedure for determining energetically favourable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28, 849-857
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 7
    • 0036406643 scopus 로고    scopus 로고
    • New Method to Detect Related Function among Proteins Independent of Sequence and Fold Homology
    • Schmitt, S.; Kuhn, D.; Klebe, G. A. New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology J. Mol. Biol. 2002, 323, 387-406
    • (2002) J. Mol. Biol. , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.A.3
  • 8
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of Functional Sites in Protein Structures
    • Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Recognition of Functional Sites in Protein Structures J. Mol. Biol. 2004, 339, 607-633
    • (2004) J. Mol. Biol. , vol.339 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 9
    • 23144456254 scopus 로고    scopus 로고
    • SiteEngines: Recognition and comparison of binding sites and protein-protein interfaces
    • Shulman-Peleg, A?; Nussinov, R.; Wolfson, H. J. SiteEngines: recognition and comparison of binding sites and protein-protein interfaces Nucleic Acids Res. 2005, 33, W337-W341
    • (2005) Nucleic Acids Res. , vol.33
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 10
    • 0037661398 scopus 로고    scopus 로고
    • Geourjon, C.A new bioinformatic approach to detect common 3D sites in protein structures
    • Jambon, M.; Imberty, A.; Delage, G. Geourjon, C.A new bioinformatic approach to detect common 3D sites in protein structures Proteins: Struct., Funct., Genet. 2003, 52, 137-145
    • (2003) Proteins: Struct., Funct., Genet. , vol.52 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Delage, G.3
  • 11
    • 65249170904 scopus 로고    scopus 로고
    • Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family
    • Kinnings, S. L.; Jackson, R. M. Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family J. Chem. Inf. Model. 2009, 49, 318-329
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 318-329
    • Kinnings, S.L.1    Jackson, R.M.2
  • 12
    • 49649083383 scopus 로고    scopus 로고
    • Detection of 3D atomic similarities and their use in the discrimination of small-molecule protein-binding sites
    • Najmanovich, R.; Kurbatova, N.; Thornton, J. Detection of 3D atomic similarities and their use in the discrimination of small-molecule protein-binding sites Bioinformatics 2008, 24, i105-i111
    • (2008) Bioinformatics , vol.24
    • Najmanovich, R.1    Kurbatova, N.2    Thornton, J.3
  • 13
    • 70449534683 scopus 로고    scopus 로고
    • The protein meta-structure: A novel concept for chemical and molecular biology
    • Konrat, R. The protein meta-structure: a novel concept for chemical and molecular biology Cell. Mol. Life Sci. 2009, 66, 3625-3639
    • (2009) Cell. Mol. Life Sci. , vol.66 , pp. 3625-3639
    • Konrat, R.1
  • 17
    • 0036682301 scopus 로고    scopus 로고
    • Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571)
    • Nagar, B.; Bornmann, W. G.; Pellicena, P.; Schindler, T.; Veach, D. R.; Miller, W. T.; Clarkson, B.; Kuriyan, J. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571) Cancer Res. 2002, 62, 4236-4243
    • (2002) Cancer Res. , vol.62 , pp. 4236-4243
    • Nagar, B.1    Bornmann, W.G.2    Pellicena, P.3    Schindler, T.4    Veach, D.R.5    Miller, W.T.6    Clarkson, B.7    Kuriyan, J.8
  • 18
    • 33847659183 scopus 로고    scopus 로고
    • C-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty
    • Seeliger, M. A.; Nagar, B.; Frank, F.; Cao, X.; Henderson, M. N.; Kuriyan, J. c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a d?stributed thermodynamic penalty Structure 2007, 15, 299-311
    • (2007) Structure , vol.15 , pp. 299-311
    • Seeliger, M.A.1    Nagar, B.2    Frank, F.3    Cao, X.4    Henderson, M.N.5    Kuriyan, J.6
  • 21
    • 77956021436 scopus 로고    scopus 로고
    • The mnist database of handwritten digits. (accessed Feb 1)
    • Le Cun, Y.; Cortes, C. The mnist database of handwritten digits. http://yann.lecun.com/exdb/mnist/ (accessed Feb 1, 2010).
    • (2010)
    • Le Cun, Y.1    Cortes, C.2
  • 22
    • 4444343398 scopus 로고    scopus 로고
    • Alignment of three-dimensional molecules using an image recognition algorithm
    • Richmond, N. J.; Willett, P.; Clark, R. D. Alignment of three-dimensional molecules using an image recognition algorithm J. Mol. Graphics Modell. 2004, 23, 199-209
    • (2004) J. Mol. Graphics Modell. , vol.23 , pp. 199-209
    • Richmond, N.J.1    Willett, P.2    Clark, R.D.3
  • 23
    • 84860428591 scopus 로고
    • Extensions of the Procrustes method for the optimal superimposition of landmarks
    • Rohlf, F. J.; Slice, D. Extensions of the Procrustes method for the optimal superimposition of landmarks Syst. Zool. 1990, 39, 40-59
    • (1990) Syst. Zool. , vol.39 , pp. 40-59
    • Rohlf, F.J.1    Slice, D.2
  • 24
    • 77956032304 scopus 로고    scopus 로고
    • version May 2009; Molecular Discovery LTD: London, U.K.. Molecular Discovery. (accessed July 1, 2009)
    • Flap, version May 2009; Molecular Discovery LTD: London, U.K.. Molecular Discovery. http://www.moldiscovery.com (accessed July 1, 2009).
    • Flap
  • 25
    • 0023173192 scopus 로고
    • A shortest augmenting path algorithm for dense and sparse linear assignment problems
    • Jonker, R.; Volgenant, A. A shortest augmenting path algorithm for dense and sparse linear assignment problems Computing 1987, 38, 325-340
    • (1987) Computing , vol.38 , pp. 325-340
    • Jonker, R.1    Volgenant, A.2
  • 28
    • 41349084852 scopus 로고    scopus 로고
    • Bias, reporting, and sharing: Computational evaluations of docking methods
    • Jain, A. N. Bias, ?eporting, and sharing: computational evaluations of docking methods J. Comput.-Aided Mol. Des. 2008, 22, 201-212
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 201-212
    • Jain, A.N.1
  • 30
    • 0041466445 scopus 로고    scopus 로고
    • Specific targeted therapy of chronic myelogenous leukemia with imatinib
    • Deininger, M. W.; Druker, B. J. Specific targeted therapy of chronic myelogenous leukemia with imatinib Pharmacol. Rev. 2003, 55, 401-423
    • (2003) Pharmacol. Rev. , vol.55 , pp. 401-423
    • Deininger, M.W.1    Druker, B.J.2
  • 32
    • 5044236233 scopus 로고    scopus 로고
    • Sequence and structural analysis of kinase ATP pocket residues
    • Vulpetti, A.; Bosotti, R. Sequence and structural analysis of kinase ATP pocket residues Il Farmaco 2004, 59, 759-765
    • (2004) Il Farmaco , vol.59 , pp. 759-765
    • Vulpetti, A.1    Bosotti, R.2
  • 35
    • 33646855259 scopus 로고    scopus 로고
    • version 7.5; Accelrys: San Diego, CA, 2008. Accelrys Pipeline Pilot (accessed July 1)
    • Pipeline Pilot, version 7.5; Accelrys: San Diego, CA, 2008. Accelrys Pipeline Pilot http://accelrys.com/products/pipeline-pilot/ (accessed July 1, 2009).
    • (2009) Pipeline Pilot
  • 37
    • 0036332629 scopus 로고    scopus 로고
    • Pharmacology of phosphodiesterase-5 inhibitors
    • Corbin, J. D.; Francis, S. H. Pharmacology of phosphodiesterase-5 inhibitors Int. J. Clin. Pract. 2002, 56, 453-459
    • (2002) Int. J. Clin. Pract. , vol.56 , pp. 453-459
    • Corbin, J.D.1    Francis, S.H.2
  • 38
    • 32544441940 scopus 로고    scopus 로고
    • New progestagens for contraceptive use
    • Sitruk-Ware, R. New progestagens for contraceptive use Human Reprod. Update 2006, 12, 169-178
    • (2006) Human Reprod. Update , vol.12 , pp. 169-178
    • Sitruk-Ware, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.