메뉴 건너뛰기




Volumn 51, Issue 8, 2011, Pages 1931-1941

Conserved core substructures in the overlay of protein-ligand complexes

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; COMPLEXATION; MULTIMEDIA SYSTEMS; PROTEINS;

EID: 80051956026     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100475y     Document Type: Article
Times cited : (13)

References (49)
  • 1
    • 33847381100 scopus 로고    scopus 로고
    • A decade of fragment-based drug design: Strategic advances and lessons learned
    • DOI 10.1038/nrd2220, PII NRD2220
    • Hajduk, P. J.; Greer, J. A decade of fragment-based drug design: strategic advances and lessons learned Nat. Rev. Drug Discovery 2007, 6, 211-219 (Pubitemid 46344625)
    • (2007) Nature Reviews Drug Discovery , vol.6 , Issue.3 , pp. 211-219
    • Hajduk, P.J.1    Greer, J.2
  • 2
    • 37549048176 scopus 로고    scopus 로고
    • Fragment-based approaches to enzyme inhibition
    • Ciulli, A.; Abell, C. Fragment-based approaches to enzyme inhibition Curr. Opin. Biotechnol. 2007, 18, 489-496
    • (2007) Curr. Opin. Biotechnol. , vol.18 , pp. 489-496
    • Ciulli, A.1    Abell, C.2
  • 6
    • 2442647742 scopus 로고    scopus 로고
    • BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, P38, and HIV protease
    • DOI 10.1021/jm030543u
    • Pierce, A. C.; Rao, G.; Bemis, G. W. BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease J. Med. Chem. 2004, 47, 2768-2775 (Pubitemid 38656730)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.11 , pp. 2768-2775
    • Pierce, A.C.1    Rao, G.2    Bemis, G.W.3
  • 7
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch, W. A discussion of the solution for the best rotation to relate two sets of vectors Acta Crystallogr., Sect. A: Found. Crystallogr. 1978, A34, 827-828
    • (1978) Acta Crystallogr., Sect. A: Found. Crystallogr. , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 9
    • 3242881211 scopus 로고    scopus 로고
    • SuperPose: A simple server for sophisticated structural superposition
    • Web Server Issue
    • Maiti, R.; Van Domselaar, G. H.; Zhang, H.; Wishart, D. S. SuperPose: a simple server for sophisticated structural superposition Nucleic Acids Res. 2004, 32 (Web Server issue) W590-W594
    • (2004) Nucleic Acids Res. , vol.32
    • Maiti, R.1    Van Domselaar, G.H.2    Zhang, H.3    Wishart, D.S.4
  • 10
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • DOI 10.1107/S0907444904026460
    • Krissinel, E.; Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 2256-2268 (Pubitemid 41742778)
    • (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.12 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 11
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov, I. N.; Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 1998, 11, 739-747 (Pubitemid 28434482)
    • (1998) Protein Engineering , vol.11 , Issue.9 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 12
    • 0042622381 scopus 로고    scopus 로고
    • A method for finding 3D similarities in protein structures
    • Zemla, A. LGA A method for finding 3D similarities in protein structures Nucleic Acids Res. 2003, 31, 3370-3374
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3370-3374
    • Zemla, A.L.1
  • 13
    • 33947532192 scopus 로고    scopus 로고
    • CAALIGN: A program for pairwise and multiple protein-structure alignment
    • DOI 10.1107/S0907444907000844, PII S0907444907000844
    • Oldfield, T. J. CAALIGN: a program for pairwise and multiple protein-structure alignment Acta Crystallogr., Sect. D: Biol. Crystallogr. 2007, 63, 514-525 (Pubitemid 46465947)
    • (2007) Acta Crystallographica Section D: Biological Crystallography , vol.63 , Issue.4 , pp. 514-525
    • Oldfield, T.J.1
  • 14
    • 25144458667 scopus 로고    scopus 로고
    • A new progressive-iterative algorithm for multiple structure alignment
    • DOI 10.1093/bioinformatics/bti527
    • Lupyan, D.; Leo-Macias, A.; Ortiz, A. R. A new progressive-iterative algorithm for multiple structure alignment Bioinformatics 2005, 21, 3255-3263 (Pubitemid 41418439)
    • (2005) Bioinformatics , vol.21 , Issue.15 , pp. 3255-3263
    • Lupyan, D.1    Leo-Macias, A.2    Ortiz, A.R.3
  • 16
    • 0142143332 scopus 로고    scopus 로고
    • MASS: Multiple structural alignment by secondary structures
    • Dror, O.; Benyamini, H.; Nussinov, R.; Wolfson, H. MASS: multiple structural alignment by secondary structures Bioinformatics 2003, 19 (Suppl 1) i95-i104
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Dror, O.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.4
  • 17
    • 0031938039 scopus 로고    scopus 로고
    • Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
    • Gerstein, M.; Levitt, M. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins Protein Sci. 1998, 7, 445-456 (Pubitemid 28092867)
    • (1998) Protein Science , vol.7 , Issue.2 , pp. 445-456
    • Gerstein, M.1    Levitt, M.2
  • 18
    • 0028150923 scopus 로고
    • Multiple protein structure alignment
    • Taylor, W. R.; Flores, T. P.; Orengo, C. A. Multiple protein structure alignment Protein Sci. 1994, 3, 1858-1870 (Pubitemid 24356609)
    • (1994) Protein Science , vol.3 , Issue.10 , pp. 1858-1870
    • Taylor, W.R.1    Flores, T.P.2    Orengo, C.A.3
  • 19
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • DOI 10.1006/jmbi.1993.1626
    • Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 1993, 234, 779-815 (Pubitemid 24007801)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 20
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
    • Russell, R. B.; Barton, G. J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels Proteins 1992, 14, 309-323
    • (1992) Proteins , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.J.2
  • 21
    • 33744808287 scopus 로고    scopus 로고
    • Comparing programs for rigid-body multiple structural superposition of proteins
    • DOI 10.1017/S0016672306248250
    • Hill, A. D.; Reilly, P. J. Comparing programs for rigid-body multiple structural superposition of proteins Proteins 2006, 64, 219-226 (Pubitemid 43831000)
    • (2006) Proteins: Structure, Function and Genetics , vol.64 , Issue.1 , pp. 219-226
    • Hill, A.D.1    Reilly, P.J.2
  • 22
    • 33644876699 scopus 로고    scopus 로고
    • SitesBase: A database for structure-based protein-ligand binding site comparisons
    • Database Issue
    • Gold, N. D.; Jackson, R. M. SitesBase: a database for structure-based protein-ligand binding site comparisons Nucleic Acids Res. 2006, 34 (Database issue) D231-D234
    • (2006) Nucleic Acids Res. , vol.34
    • Gold, N.D.1    Jackson, R.M.2
  • 23
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • DOI 10.1016/j.jmb.2004.04.012, PII S0022283604004139
    • Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Recognition of functional sites in protein structures J. Mol. Biol. 2004, 339, 607-633 (Pubitemid 38625909)
    • (2004) Journal of Molecular Biology , vol.339 , Issue.3 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 25
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • DOI 10.1016/S0022-2836(02)00811-2
    • 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 (Pubitemid 35283699)
    • (2002) Journal of Molecular Biology , vol.323 , Issue.2 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 26
    • 0037436333 scopus 로고    scopus 로고
    • Utilising structural knowledge in drug design strategies: Applications using relibase
    • DOI 10.1016/S0022-2836(02)01409-2
    • Günther, J.; Bergner, A.; Hendlich, M.; Klebe, G. Utilising structural knowledge in drug design strategies: applications using Relibase J. Mol. Biol. 2003, 326, 621-636 (Pubitemid 36279353)
    • (2003) Journal of Molecular Biology , vol.326 , Issue.2 , pp. 621-636
    • Gunther, J.1    Bergner, A.2    Hendlich, M.3    Klebe, G.4
  • 27
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Database Issue
    • Porter, C. T.; Bartlett, G. J.; Thornton, J. M. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Res. 2004, 32 (Database issue) D129-D133
    • (2004) Nucleic Acids Res. , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 28
    • 34848848829 scopus 로고    scopus 로고
    • Automatic generation of 3D motifs for classification of protein binding sites
    • Nebel, J.-C.; Herzyk, P.; Gilbert, D. R. Automatic generation of 3D motifs for classification of protein binding sites BMC Bioinformatics 2007, 8, 321
    • (2007) BMC Bioinformatics , vol.8 , pp. 321
    • Nebel, J.-C.1    Herzyk, P.2    Gilbert, D.R.3
  • 30
    • 79951773256 scopus 로고    scopus 로고
    • Structural Signatures of Enzyme Binding Pockets from Order-Independent Surface Alignment: A Study of Metalloendopeptidase and NAD Binding Proteins
    • Dundas, J.; Adamian, L.; Liang, J. Structural Signatures of Enzyme Binding Pockets from Order-Independent Surface Alignment: A Study of Metalloendopeptidase and NAD Binding Proteins J. Mol. Biol. 2011, 406, 713-729
    • (2011) J. Mol. Biol. , vol.406 , pp. 713-729
    • Dundas, J.1    Adamian, L.2    Liang, J.3
  • 32
    • 0030817619 scopus 로고    scopus 로고
    • LORE: Exploiting database of known structures
    • DOI 10.1016/S0076-6879(97)77014-9
    • Finzel, B. LORE: exploiting database of known structures Methods Enzymol. 1997, 277, 230-242 (Pubitemid 27390924)
    • (1997) Methods in Enzymology , vol.277 , pp. 230-242
    • Finzel, B.C.1
  • 33
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones, T. A.; Thirup, S. Using known substructures in protein model building and crystallography EMBO J. 1986, 5, 819-822
    • (1986) EMBO J. , vol.5 , pp. 819-822
    • Jones, T.A.1    Thirup, S.2
  • 36
    • 0037032835 scopus 로고    scopus 로고
    • The protein kinase complement of the human genome
    • DOI 10.1126/science.1075762
    • Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome Science 2002, 298, 1912-1934 (Pubitemid 35425239)
    • (2002) Science , vol.298 , Issue.5600 , pp. 1912-1934
    • Manning, G.1    Whyte, D.B.2    Martinez, R.3    Hunter, T.4    Sudarsanam, S.5
  • 37
    • 80052015280 scopus 로고    scopus 로고
    • Schrödinger, LLC: Cambridge, MA; Accessed January 15.
    • Delano, W. Introduction to PyMol; Schrödinger, LLC: Cambridge, MA; http://www.pymol.org/. Accessed January 15, 2010.
    • (2010) Introduction to PyMol
    • Delano, W.1
  • 43
    • 39749162787 scopus 로고    scopus 로고
    • Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: Structure of lck/imatinib complex
    • DOI 10.1002/prot.21633
    • Jacobs, M. D.; Caron, P. R.; Hare, B. J. Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex Proteins 2008, 70, 1451-1460 (Pubitemid 351304103)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.4 , pp. 1451-1460
    • Jacobs, M.D.1    Caron, P.R.2    Hare, B.J.3
  • 44
    • 18044365802 scopus 로고    scopus 로고
    • Conformational adaptation of nuclear receptor ligand binding domains to agonists: Potential for novel approaches to ligand design
    • DOI 10.1016/j.jsbmb.2005.01.004, Proceedings of the 16th Internatioanl Symposium of the Journal of Steroid Biochemistry and Molecular Biology
    • Togashi, M.; Borngraeber, S.; Sandler, B.; Fletterick, R. J.; Webb, P.; Baxter, J. D. Conformational adaptation of nuclear receptor ligand binding domains to agonists: potential for novel approaches to ligand design J. Steroid Biochem. Mol. Biol. 2005, 93, 127-137 (Pubitemid 40602485)
    • (2005) Journal of Steroid Biochemistry and Molecular Biology , vol.93 , Issue.2-5 , pp. 127-137
    • Togashi, M.1    Borngraeber, S.2    Sandler, B.3    Fletterick, R.J.4    Webb, P.5    Baxter, J.D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.