메뉴 건너뛰기




Volumn 21, Issue 8, 2005, Pages 1479-1486

Architecture of basic building blocks in protein and domain structural interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; HUMAN; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; YEAST;

EID: 17444391730     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti240     Document Type: Article
Times cited : (23)

References (42)
  • 1
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • Aloy,P., Ceulemans,H., Stark,A. and Russell,R.B. (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    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 2
    • 5044235050 scopus 로고    scopus 로고
    • The thousand interactions for the molecular biologist
    • Aloy,P. and Russell,R.B. (2004) The thousand interactions for the molecular biologist. Nat. Biotechnol., 22, 1317-1321.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1317-1321
    • Aloy, P.1    Russell, R.B.2
  • 5
    • 17444365746 scopus 로고    scopus 로고
    • Biological network evolution hypothesis applied to protein structural interactome
    • Bolser,D. and Park,J. (2003) Biological network evolution hypothesis applied to protein structural interactome. Genomics Inform. 1, 7-19.
    • (2003) Genomics Inform. , vol.1 , pp. 7-19
    • Bolser, D.1    Park, J.2
  • 6
    • 2942610863 scopus 로고    scopus 로고
    • Visualisation and graph - Theoretic analysis of a large-scale protein structural interactome
    • Bolser,D., Dafas,P., Harrington,R., Park,J. and Schroeder,M. (2003) Visualisation and graph - theoretic analysis of a large-scale protein structural interactome. BMC Bioinformatics, 4, 45-76.
    • (2003) BMC Bioinformatics , vol.4 , pp. 45-76
    • Bolser, D.1    Dafas, P.2    Harrington, R.3    Park, J.4    Schroeder, M.5
  • 7
    • 0345447447 scopus 로고    scopus 로고
    • Eukaryotic domain evolution inferred from genome comparisons
    • Copley,P.R., Goodstadt,L. and Ponting,C. (2003) Eukaryotic domain evolution inferred from genome comparisons. Curr. Opin. Genet. Dev., 13, 623-628.
    • (2003) Curr. Opin. Genet. Dev. , vol.13 , pp. 623-628
    • Copley, P.R.1    Goodstadt, L.2    Ponting, C.3
  • 8
    • 3543090867 scopus 로고    scopus 로고
    • Using convex hulls to extract interaction interfaces from known structures
    • Dafas,P., Bolser,D., Gomoluch,J., Park,J. and Schroeder,M. (2004) Using convex hulls to extract interaction interfaces from known structures. Bioinformatics, 20, 1486-1490.
    • (2004) Bioinformatics , vol.20 , pp. 1486-1490
    • Dafas, P.1    Bolser, D.2    Gomoluch, J.3    Park, J.4    Schroeder, M.5
  • 9
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domain-domain interactions from protein-protein interactions
    • Deng,M., Mehta,S., Sun,F. and Chen,T. (2002a) Inferring domain-domain interactions from protein-protein interactions. Genome Res., 12, 1540-1548.
    • (2002) Genome Res. , vol.12 , pp. 1540-1548
    • Deng, M.1    Mehta, S.2    Sun, F.3    Chen, T.4
  • 11
    • 0036805329 scopus 로고    scopus 로고
    • Bridging structural biology and genomics: Assessing protein interaction data with known complexes
    • Edwards,A.M., Kus,B., Jansen,R., Greenbaum,D., Greenblatt,J. and Gerstein,M. (2002) Bridging structural biology and genomics: assessing protein interaction data with known complexes, Trends Genet. 18, 529-536.
    • (2002) Trends Genet. , vol.18 , pp. 529-536
    • Edwards, A.M.1    Kus, B.2    Jansen, R.3    Greenbaum, D.4    Greenblatt, J.5    Gerstein, M.6
  • 12
    • 0036435908 scopus 로고    scopus 로고
    • Co-evolutionary analysis reveals insight into protein-protein interactions
    • Goh,C. and Cohen,F. (2002) Co-evolutionary analysis reveals insight into protein-protein interactions. J. Mol. Biol., 324 177-192.
    • (2002) J. Mol. Biol. , vol.324 , pp. 177-192
    • Goh, C.1    Cohen, F.2
  • 13
    • 0034595516 scopus 로고    scopus 로고
    • Co-evolution of proteins with their interaction partners
    • Goh,C., Bogan,A., Joachimiak,M., Walther,D. and Cohen,F. (2000) Co-evolution of proteins with their interaction partners. J. Mol. Biol., 299, 283-293.
    • (2000) J. Mol. Biol. , vol.299 , pp. 283-293
    • Goh, C.1    Bogan, A.2    Joachimiak, M.3    Walther, D.4    Cohen, F.5
  • 14
    • 17444370858 scopus 로고    scopus 로고
    • HPID: The Human Protein Interaction Database
    • Han,K., Park,B., Kim,H., Hong,J. and Park,J. (2004) HPID: the Human Protein Interaction Database. Bioinformatics, 20, 303-305.
    • (2004) Bioinformatics , vol.20 , pp. 303-305
    • Han, K.1    Park, B.2    Kim, H.3    Hong, J.4    Park, J.5
  • 16
    • 0028915169 scopus 로고
    • Different evolutionary histories of kringle and protease domains in serine proteases: A typical example of domain evolution
    • Ikeo,K., Takahashi,K. and Gojobori,T. (1995) Different evolutionary histories of kringle and protease domains in serine proteases: a typical example of domain evolution, J. Mol. Evol., 40, 177-192.
    • (1995) J. Mol. Evol. , vol.40 , pp. 177-192
    • Ikeo, K.1    Takahashi, K.2    Gojobori, T.3
  • 18
    • 0033974688 scopus 로고    scopus 로고
    • Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    • Ito,T., Tashiro,K., Muta,S., Ozawa,R., Chiba,T., Nishizawa,M., Yamamoto,K., Kuhara,S. and Sakaki,Y. (2000) Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins, Proc. Natl Acad. Sci. USA, 97, 1143-1147.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 1143-1147
    • Ito, T.1    Tashiro, K.2    Muta, S.3    Ozawa, R.4    Chiba, T.5    Nishizawa, M.6    Yamamoto, K.7    Kuhara, S.8    Sakaki, Y.9
  • 19
    • 0037311772 scopus 로고    scopus 로고
    • Visualization and analysis of protein interactions
    • Ju,B.H., Park,B., Park,J. and Han,K. (2003) Visualization and analysis of protein interactions. Bioinformatics, 19, 317-318.
    • (2003) Bioinformatics , vol.19 , pp. 317-318
    • Ju, B.H.1    Park, B.2    Park, J.3    Han, K.4
  • 20
    • 2442646432 scopus 로고    scopus 로고
    • Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
    • Kim,W.K., Bolser,D. and Park,J. (2004) Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics, 20 1138-1150.
    • (2004) Bioinformatics , vol.20 , pp. 1138-1150
    • Kim, W.K.1    Bolser, D.2    Park, J.3
  • 21
    • 7444243253 scopus 로고    scopus 로고
    • Predicting protein interactions in human by homologous interactions in yeast
    • Kim,H., Park,J. and Han,K. (2003) Predicting protein interactions in human by homologous interactions in yeast. LNCS 2637, 159-165.
    • (2003) LNCS , vol.2637 , pp. 159-165
    • Kim, H.1    Park, J.2    Han, K.3
  • 22
    • 0642343787 scopus 로고    scopus 로고
    • Large scale statistical prediction of protein-protein interaction by Potentially Interacting Domain (PID) Pair
    • Kim,W.K., Park,J. and Suh,J.K. (2002) Large scale statistical prediction of protein-protein interaction by Potentially Interacting Domain (PID) Pair. Genome Inform., 13, 42-50.
    • (2002) Genome Inform. , vol.13 , pp. 42-50
    • Kim, W.K.1    Park, J.2    Suh, J.K.3
  • 23
    • 0035232248 scopus 로고    scopus 로고
    • Generating protein interaction maps from incomplete data: Application to fold assignment
    • Lappe,M., Park,J., Niggemann,O. and Holm,L. (2001) Generating protein interaction maps from incomplete data: application to fold assignment. Bioinformatics, (Suppl.), S149-S156.
    • (2001) Bioinformatics , Issue.SUPPL.
    • Lappe, M.1    Park, J.2    Niggemann, O.3    Holm, L.4
  • 24
    • 1542271409 scopus 로고    scopus 로고
    • Predicting protein function from protein/protein interaction data: A probabilistic approach
    • Letovsky,S. and Kasif,S. (2003) Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics, (Suppl.), I197-I204.
    • (2003) Bioinformatics , Issue.SUPPL.
    • Letovsky, S.1    Kasif, S.2
  • 26
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte,E., Pellegrini,M., Ng,H., Rice,D., Yeates,T. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.1    Pellegrini, M.2    Ng, H.3    Rice, D.4    Yeates, T.5    Eisenberg, D.6
  • 27
    • 0012765032 scopus 로고
    • Computing automorphisms and canonical labelling of graphs
    • McKay,B. (1978) Computing automorphisms and canonical labelling of graphs. LNM, 686, 223-232.
    • (1978) LNM , vol.686 , pp. 223-232
    • McKay, B.1
  • 30
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 31
    • 0035751865 scopus 로고    scopus 로고
    • Conservation of protein interaction network in evolution
    • Park,J. and Bolser,D. (2001) Conservation of protein interaction network in evolution. Genome Inform., 12, 135-140.
    • (2001) Genome Inform. , vol.12 , pp. 135-140
    • Park, J.1    Bolser, D.2
  • 32
    • 0035970298 scopus 로고    scopus 로고
    • Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast
    • Park,J., Lappe,M. and Teichmann,S.A. (2001) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol., 307 929-938.
    • (2001) J. Mol. Biol. , vol.307 , pp. 929-938
    • Park, J.1    Lappe, M.2    Teichmann, S.A.3
  • 33
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • Pazos,F. and Valencia,A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng., 14, 609-614.
    • (2001) Protein Eng. , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 36
    • 2442534964 scopus 로고    scopus 로고
    • Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    • San Diego, CA
    • Sharan,R., Ideker,T., Kelley,B., Shamir,R. and Karp,R. (2004) Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. In Proceedings of RECOMB2004, San Diego, CA, pp. 282-289.
    • (2004) Proceedings of RECOMB2004 , pp. 282-289
    • Sharan, R.1    Ideker, T.2    Kelley, B.3    Shamir, R.4    Karp, R.5
  • 37
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr,S., Milo,R., Mangan,S. and Alon,U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet., 31, 64-68.
    • (2002) Nat. Genet. , vol.31 , pp. 64-68
    • Shen-Orr, S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 38
    • 0032424307 scopus 로고    scopus 로고
    • Structural assignments to the proteins of Mycoplasma genitalium show that they have been formed by extensive gene duplications and domain rearrangements
    • Teichmann,S., Park,J. and Chothia,C. (1998) Structural assignments to the proteins of Mycoplasma genitalium show that they have been formed by extensive gene duplications and domain rearrangements. Proc. Natl Acad. Sci. USA, 30, 14658-14663.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.30 , pp. 14658-14663
    • Teichmann, S.1    Park, J.2    Chothia, C.3
  • 40
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • Vazquez,A., Flammini,A., Maritan,A. and Vespignani,A. (2003) Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol., 21, 697-700.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 697-700
    • Vazquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4
  • 41
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motif constituent in the yeast protein interaction network
    • Wuchty,S., Oltval,Z.N. and Barabasi,A.L. (2003) Evolutionary conservation of motif constituent in the yeast protein interaction network. Nat. Genet., 35, 176-179.
    • (2003) Nat. Genet. , vol.35 , pp. 176-179
    • Wuchty, S.1    Oltval, Z.N.2    Barabasi, A.L.3
  • 42
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios,I., Salwinski,L., Duan,X.J., Higney,P., Kim,S.M. and Eisenberg,D. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.M.5    Eisenberg, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.