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Volumn 28, Issue 3, 2012, Pages 324-330

SCPC: A method to structurally compare protein complexes

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN; MULTIPROTEIN COMPLEX;

EID: 84856578133     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr654     Document Type: Article
Times cited : (8)

References (45)
  • 1
    • 51649094321 scopus 로고    scopus 로고
    • Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains
    • Akiva, E. et al. (2008) Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Proc. Natl Acad. Sci. USA, 105, 13292-13297.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 13292-13297
    • Akiva, E.1
  • 2
    • 13444272070 scopus 로고    scopus 로고
    • The Biomolecular Interaction Network Database and related tools 2005 update
    • Alfarano, C. et al. (2005) The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res., 33, D418-D424.
    • (2005) Nucleic Acids Res , vol.33
    • Alfarano, C.1
  • 3
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • Aloy, P. et al. (2003) The relationship between sequence and interaction divergence in proteins. J. Mol. Biol., 332, 989-998.
    • (2003) J. Mol. Biol. , vol.332 , pp. 989-998
    • Aloy, P.1
  • 4
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 5
    • 34547120236 scopus 로고    scopus 로고
    • Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state
    • Andrade, J. et al. (2007) Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state. J. Biol. Chem., 282, 19598-19605.
    • (2007) J. Biol. Chem. , vol.282 , pp. 19598-19605
    • Andrade, J.1
  • 6
    • 75549087047 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2010
    • Aranda, B. et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res., 38, D525-D531.
    • (2010) Nucleic Acids Res , vol.38
    • Aranda, B.1
  • 7
    • 0018361151 scopus 로고
    • Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism
    • Baldwin, J. and Chothia, C. (1979) Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism. J. Mol. Biol., 129, 175-220.
    • (1979) J. Mol. Biol. , vol.129 , pp. 175-220
    • Baldwin, J.1    Chothia, C.2
  • 8
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
    • Berman, H. et al. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
    • (2007) Nucleic Acids Res , vol.35
    • Berman, H.1
  • 9
    • 75549083295 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2009 update
    • Ceol, A. et al. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res., 38, D532-D539.
    • (2010) Nucleic Acids Res , vol.38
    • Ceol, A.1
  • 10
    • 33746274673 scopus 로고    scopus 로고
    • Structure-stability-activity relationship in covalently crosslinked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase
    • Chiu, W.C. et al. (2006) Structure-stability-activity relationship in covalently crosslinked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J. Mol. Biol., 359, 741-753.
    • (2006) J. Mol. Biol. , vol.359 , pp. 741-753
    • Chiu, W.C.1
  • 11
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-246.
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 12
    • 0029936121 scopus 로고    scopus 로고
    • Surprising similarities in structure comparison
    • Gibrat, J.F. et al. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 377-385
    • Gibrat, J.F.1
  • 13
    • 48249130416 scopus 로고    scopus 로고
    • Novel protein folds and their nonsequential structural analogs
    • Guerler, A. and Knapp, E.W. (2008) Novel protein folds and their nonsequential structural analogs. Protein Sci., 17, 1374-1382.
    • (2008) Protein Sci , vol.17 , pp. 1374-1382
    • Guerler, A.1    Knapp, E.W.2
  • 14
    • 78650537920 scopus 로고    scopus 로고
    • Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states
    • Hashimoto, K. and Panchenko, A.R. (2010) Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. Proc. Natl Acad. Sci. USA, 107, 20352-20357.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 20352-20357
    • Hashimoto, K.1    Panchenko, A.R.2
  • 15
    • 0032169688 scopus 로고    scopus 로고
    • PQS: a protein quaternary structure file server
    • Henrick, K. and Thornton, J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 16
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 17
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito, T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 4569-4574
    • Ito, T.1
  • 18
    • 0041620359 scopus 로고    scopus 로고
    • MATRAS: a program for protein 3D structure comparison
    • Kawabata, T. (2003) MATRAS: a program for protein 3D structure comparison. Nucleic Acids Res., 31, 3367-3369.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3367-3369
    • Kawabata, T.1
  • 19
    • 0034308164 scopus 로고    scopus 로고
    • Protein structure comparison using the markov transition model of evolution
    • Kawabata, T. and Nishikawa, K. (2000) Protein structure comparison using the markov transition model of evolution. Proteins, 41, 108-122.
    • (2000) Proteins , vol.41 , pp. 108-122
    • Kawabata, T.1    Nishikawa, K.2
  • 20
    • 58149193222 scopus 로고    scopus 로고
    • Human Protein Reference Database-2009 update
    • Keshava Prasad, T.S. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
    • (2009) Nucleic Acids Res , vol.37
    • Keshava Prasad, T.S.1
  • 21
    • 0026244229 scopus 로고
    • MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
    • Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 22
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel, E. and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr., 60, 2256-2268.
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 23
    • 33751415854 scopus 로고    scopus 로고
    • 3D complex: a structural classification of protein complexes
    • Levy, E.D. et al. (2006) 3D complex: a structural classification of protein complexes. PLoS Comput. Biol., 2, e155.
    • (2006) PLoS Comput. Biol. , vol.2
    • Levy, E.D.1
  • 24
    • 46249083761 scopus 로고    scopus 로고
    • Assembly reflects evolution of protein complexes
    • Levy, E.D. et al. (2008) Assembly reflects evolution of protein complexes. Nature, 453, 1262-1265.
    • (2008) Nature , vol.453 , pp. 1262-1265
    • Levy, E.D.1
  • 25
    • 0035850791 scopus 로고    scopus 로고
    • The crystal structure of bar-headed goose hemoglobin in deoxy form: the allosteric mechanism of a hemoglobin species with high oxygen affinity
    • Liang, Y. et al. (2001) The crystal structure of bar-headed goose hemoglobin in deoxy form: the allosteric mechanism of a hemoglobin species with high oxygen affinity. J. Mol. Biol., 313, 123-137.
    • (2001) J. Mol. Biol. , vol.313 , pp. 123-137
    • Liang, Y.1
  • 26
    • 0030979555 scopus 로고    scopus 로고
    • Circular permutations of natural protein sequences: structural evidence
    • Lindqvist, Y. and Schneider, G. (1997) Circular permutations of natural protein sequences: structural evidence. Curr. Opin. Struct. Biol., 7, 422-427.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 422-427
    • Lindqvist, Y.1    Schneider, G.2
  • 27
    • 0029061843 scopus 로고
    • Comparison of spatial arrangements of secondary structural elements in proteins
    • Mizuguchi, K. and Go, N. (1995) Comparison of spatial arrangements of secondary structural elements in proteins. Protein Eng., 8, 353-362.
    • (1995) Protein Eng , vol.8 , pp. 353-362
    • Mizuguchi, K.1    Go, N.2
  • 28
    • 0033638223 scopus 로고    scopus 로고
    • Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast
    • Mossessova, E. and Lima, C.D. (2000) Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol. Cell, 5, 865-876.
    • (2000) Mol. Cell , vol.5 , pp. 865-876
    • Mossessova, E.1    Lima, C.D.2
  • 29
    • 67649869968 scopus 로고    scopus 로고
    • MM-align: a quick algorithm for aligning multiplechain protein complex structures using iterative dynamic programming
    • Mukherjee, S. and Zhang, Y. (2009) MM-align: a quick algorithm for aligning multiplechain protein complex structures using iterative dynamic programming. Nucleic Acids Res., 37, e83.
    • (2009) Nucleic Acids Res , vol.37
    • Mukherjee, S.1    Zhang, Y.2
  • 30
    • 0014757386 scopus 로고
    • Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S.B. and Wunsch, C.D. (1970)Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 31
    • 77951243441 scopus 로고    scopus 로고
    • Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state
    • Nishi, H. and Ota, M. (2010) Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state. Proteins, 78, 1563-1574.
    • (2010) Proteins , vol.78 , pp. 1563-1574
    • Nishi, H.1    Ota, M.2
  • 32
    • 79960090510 scopus 로고    scopus 로고
    • Cover and spacer insertions: small nonhydrophobic accessories that assist protein oligomerization
    • Nishi, H. et al. (2011) Cover and spacer insertions: small nonhydrophobic accessories that assist protein oligomerization. Proteins, 79, 2372-2379.
    • (2011) Proteins , vol.79 , pp. 2372-2379
    • Nishi, H.1
  • 33
    • 0029948001 scopus 로고    scopus 로고
    • SSAP: sequential structure alignment program for protein structure comparison
    • Orengo, C.A. and Taylor, W.R. (1996) SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol., 266, 617-635.
    • (1996) Methods Enzymol , vol.266 , pp. 617-635
    • Orengo, C.A.1    Taylor, W.R.2
  • 34
    • 33745571654 scopus 로고    scopus 로고
    • 1.25 Å resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms
    • Park, S.Y. et al. (2006) 1.25 Å resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. J. Mol. Biol., 360, 690-701.
    • (2006) J. Mol. Biol. , vol.360 , pp. 690-701
    • Park, S.Y.1
  • 35
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 36
    • 0015529611 scopus 로고
    • Nature of haem-haem interaction
    • Perutz, M.F. (1972) Nature of haem-haem interaction. Nature, 237, 495-499.
    • (1972) Nature , vol.237 , pp. 495-499
    • Perutz, M.F.1
  • 37
    • 9644294252 scopus 로고    scopus 로고
    • Structure of a complex between Nedd8 and the Ulp/Senp protease family member Den1
    • Reverter, D. et al. (2005) Structure of a complex between Nedd8 and the Ulp/Senp protease family member Den1. J. Mol. Biol., 345, 141-151.
    • (2005) J. Mol. Biol. , vol.345 , pp. 141-151
    • Reverter, D.1
  • 38
    • 0347755535 scopus 로고    scopus 로고
    • The Database of Interacting Proteins: 2004 update
    • Salwinski, L. et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
    • (2004) Nucleic Acids Res , vol.32
    • Salwinski, L.1
  • 39
    • 77951248793 scopus 로고    scopus 로고
    • Circular permuted proteins in the universe of protein folds
    • Schmidt-Goenner, T. et al. (2010) Circular permuted proteins in the universe of protein folds. Proteins, 78, 1618-1630.
    • (2010) Proteins , vol.78 , pp. 1618-1630
    • Schmidt-Goenner, T.1
  • 40
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov, I.N. and Bourne, P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 41
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 42
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1
  • 43
    • 0030582681 scopus 로고    scopus 로고
    • The crystal structure of horse deoxyhaemoglobin trapped in the high-affinity (R) state
    • Wilson, J. et al. (1996) The crystal structure of horse deoxyhaemoglobin trapped in the high-affinity (R) state. J. Mol. Biol., 264, 743-756.
    • (1996) J. Mol. Biol. , vol.264 , pp. 743-756
    • Wilson, J.1
  • 44
    • 16344379369 scopus 로고    scopus 로고
    • Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
    • Yuan, X. and Bystroff, C. (2005) Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics, 21, 1010-1019.
    • (2005) Bioinformatics , vol.21 , pp. 1010-1019
    • Yuan, X.1    Bystroff, C.2
  • 45
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • Zhang, Y. and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


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