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Volumn 24, Issue 16, 2008, Pages

An integrative approach for predicting interactions of protein regions

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS; CONFERENCE PAPER; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; HUMAN; MATHEMATICAL COMPUTING; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; VALIDATION STUDY;

EID: 49549092736     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn290     Document Type: Conference Paper
Times cited : (12)

References (61)
  • 1
    • 27544487034 scopus 로고    scopus 로고
    • Decomposing protein networks into domain-domain interactions
    • Albrecht,M. et al. (2005) Decomposing protein networks into domain-domain interactions. Bioinformatics, 21 (Suppl. 2), ii220-ii221.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Albrecht, M.1
  • 2
    • 33644550021 scopus 로고    scopus 로고
    • Structural systems biology: Modelling protein interactions
    • Aloy,P. and Russell,R. (2006) Structural systems biology: Modelling protein interactions. Nat. Rev. Mol. Cell Biol., 7, 188-197.
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.2
  • 3
    • 42449161827 scopus 로고    scopus 로고
    • The interface of protein-protein complexes: Analysis of contacts and prediction of interactions
    • Bahadur,R.P. and Zacharias,M. (2007) The interface of protein-protein complexes: Analysis of contacts and prediction of interactions. Cell. Mol. Life Sci., 65, 1059-1072.
    • (2007) Cell. Mol. Life Sci , vol.65 , pp. 1059-1072
    • Bahadur, R.P.1    Zacharias, M.2
  • 4
    • 9144257886 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Bateman,A. et al. (2003) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
    • (2003) Nucleic Acids Res , vol.32
    • Bateman, A.1
  • 5
    • 0345059376 scopus 로고    scopus 로고
    • Announcing the worldwide Protein Data Bank
    • Berman,H. et al. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980.
    • (2003) Nat. Struct. Biol , vol.10 , pp. 980
    • Berman, H.1
  • 6
    • 33746363486 scopus 로고    scopus 로고
    • Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits
    • Bhattacharyya,R.P. et al. (2006) Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem., 75, 655-680.
    • (2006) Annu. Rev. Biochem , vol.75 , pp. 655-680
    • Bhattacharyya, R.P.1
  • 7
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • Bock,J. and Gough,D. (2001) Predicting protein-protein interactions from primary structure. Bioinfonnatics, 17, 455-460.
    • (2001) Bioinfonnatics , vol.17 , pp. 455-460
    • Bock, J.1    Gough, D.2
  • 8
    • 15044350197 scopus 로고    scopus 로고
    • The evolution of domain arrangements in proteins and interaction networks
    • Bornberg-Baucr,E. et al. (2005) The evolution of domain arrangements in proteins and interaction networks. Cell. Mol. Life Sci., 62, 435-445.
    • (2005) Cell. Mol. Life Sci , vol.62 , pp. 435-445
    • Bornberg-Baucr, E.1
  • 9
    • 33846102842 scopus 로고    scopus 로고
    • DOMINO: A database of domain-peptide interactions
    • Ceol,A. et al. (2006) DOMINO: A database of domain-peptide interactions. Nucleic Acids Res., 35, D557-D560.
    • (2006) Nucleic Acids Res , vol.35
    • Ceol, A.1
  • 10
    • 33846073818 scopus 로고    scopus 로고
    • MINT: The Molecular INTeraction database
    • Chatr-aryamontri,A. et al. (2007) MINT: The Molecular INTeraction database. Nucleic Acids Res., 35, D572-D574.
    • (2007) Nucleic Acids Res , vol.35
    • Chatr-aryamontri, A.1
  • 11
    • 33644835242 scopus 로고    scopus 로고
    • Inferring protein interactions from experimental data by association probabilistic method
    • Chen,L. et al. (2006) Inferring protein interactions from experimental data by association probabilistic method. Proteins, 62, 833-837.
    • (2006) Proteins , vol.62 , pp. 833-837
    • Chen, L.1
  • 12
    • 28944450149 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions using random decision forest framework
    • Chen,X. and Liu,M. (2005) Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 21, 4394-4400.
    • (2005) Bioinformatics , vol.21 , pp. 4394-4400
    • Chen, X.1    Liu, M.2
  • 13
    • 38449100072 scopus 로고    scopus 로고
    • The Protein Identifier Cross-Reference (PICR) service: Reconciling protein identifiers across multiple source databases
    • Cote,R.G. et al. (2007) The Protein Identifier Cross-Reference (PICR) service: Reconciling protein identifiers across multiple source databases. BMC Bioinformatics, 8, 401.
    • (2007) BMC Bioinformatics , vol.8 , pp. 401
    • Cote, R.G.1
  • 14
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm
    • Dempster,A. et al. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. Ser. B, 39, 1-38.
    • (1977) J. R. Stat. Soc. Ser. B , vol.39 , pp. 1-38
    • Dempster, A.1
  • 15
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domain-domain interactions from protein-protein interactions
    • Deng,M. et al. (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res., 12, 1540-1548.
    • (2002) Genome Res , vol.12 , pp. 1540-1548
    • Deng, M.1
  • 16
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson,H.J. and Wright,P.E. (2005) Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol., 6, 197-208.
    • (2005) Nat. Rev. Mol. Cell Biol , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 17
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright,A.J. et al. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1
  • 18
    • 13844264506 scopus 로고    scopus 로고
    • iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    • Finn,R. et al. (2004) iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21, 410-412.
    • (2004) Bioinformatics , vol.21 , pp. 410-412
    • Finn, R.1
  • 19
    • 33644876020 scopus 로고    scopus 로고
    • Pfam: Clans, web tools and services
    • Finn,R. et al. (2005) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
    • (2005) Nucleic Acids Res , vol.34
    • Finn, R.1
  • 20
    • 0036360139 scopus 로고    scopus 로고
    • Towards the prediction of complete protein-protein interaction networks
    • Gomez,S. and Rzhetsky,A. (2002) Towards the prediction of complete protein-protein interaction networks. Pac. Symp. Biocomput., 413-424.
    • (2002) Pac. Symp. Biocomput , pp. 413-424
    • Gomez, S.1    Rzhetsky, A.2
  • 21
    • 33847753484 scopus 로고    scopus 로고
    • Predicting domain-domain interactions using a parsimony approach
    • Guimaraes,K. et al. (2006) Predicting domain-domain interactions using a parsimony approach. Genome Biol., 7, R104.
    • (2006) Genome Biol , vol.7
    • Guimaraes, K.1
  • 22
    • 42949163440 scopus 로고    scopus 로고
    • Interrogating domain-domain interactions with parsimony based approaches
    • Guimaraes,K.S. and Przytycka,T.M. (2008) Interrogating domain-domain interactions with parsimony based approaches. BMC Bioinformatics, 9, 171.
    • (2008) BMC Bioinformatics , vol.9 , pp. 171
    • Guimaraes, K.S.1    Przytycka, T.M.2
  • 23
    • 4544222482 scopus 로고    scopus 로고
    • A domain combination based probabilistic framework for protein-protein interaction prediction
    • Han,D. et al. (2005) A domain combination based probabilistic framework for protein-protein interaction prediction. Genome Informatics, 14, 250-259.
    • (2005) Genome Informatics , vol.14 , pp. 250-259
    • Han, D.1
  • 24
    • 18244400278 scopus 로고    scopus 로고
    • A simple method for inferring strengths of protein-protein interactions
    • Hayashida,M. et al. (2005) A simple method for inferring strengths of protein-protein interactions. Genome Informatics, 15, 56-68.
    • (2005) Genome Informatics , vol.15 , pp. 56-68
    • Hayashida, M.1
  • 25
    • 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
  • 26
    • 33847720776 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from protein domains using a set cover approach
    • Huang,C. et al. (2007) Predicting protein-protein interactions from protein domains using a set cover approach. IEEE/ACM Trans. Comput. Biol. Bioinform., 4, 78-87.
    • (2007) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.4 , pp. 78-87
    • Huang, C.1
  • 27
    • 19344372749 scopus 로고    scopus 로고
    • Gene duplication: The genomic trade in spare parts
    • Hurles,M. (2004) Gene duplication: The genomic trade in spare parts. PLoS Biol., 2, E206.
    • (2004) PLoS Biol , vol.2
    • Hurles, M.1
  • 28
    • 34249730066 scopus 로고    scopus 로고
    • Evolutionary conservation of domain-domain interactions
    • Itzhaki,Z. et al. (2006) Evolutionary conservation of domain-domain interactions. Genome Biol., 7, R125.
    • (2006) Genome Biol , vol.7
    • Itzhaki, Z.1
  • 29
    • 33748333117 scopus 로고    scopus 로고
    • Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
    • Jothi,R. et al. (2006) Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J. Mol. Biol., 362, 861-875.
    • (2006) J. Mol. Biol , vol.362 , pp. 861-875
    • Jothi, R.1
  • 30
    • 34248513211 scopus 로고    scopus 로고
    • Predicting protein domain interactions from coevolution of conserved regions
    • Kann,M. et al. (2007) Predicting protein domain interactions from coevolution of conserved regions. Proteins, 67, 811-820.
    • (2007) Proteins , vol.67 , pp. 811-820
    • Kann, M.1
  • 31
    • 33846047770 scopus 로고    scopus 로고
    • IntAct - open source resource for molecular interaction data
    • Kerrien,S. et al. (2007) IntAct - open source resource for molecular interaction data. Nucleic Acids Res., 35, D561-D565.
    • (2007) Nucleic Acids Res , vol.35
    • Kerrien, S.1
  • 32
    • 0642343787 scopus 로고    scopus 로고
    • Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair
    • Kim,W. et al. (2003) Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. Genome Informatics, 13, 42-50.
    • (2003) Genome Informatics , vol.13 , pp. 42-50
    • Kim, W.1
  • 33
    • 33745327144 scopus 로고    scopus 로고
    • An integrated approach to the prediction of domain-domain interactions
    • Lee,H. et al. (2006) An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7, 269.
    • (2006) BMC Bioinformatics , vol.7 , pp. 269
    • Lee, H.1
  • 34
    • 25144479967 scopus 로고    scopus 로고
    • Inferring protein-protein interactions through high-throughput interaction data from diverse organisms
    • Liu,Y. et al. (2005) Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics, 21, 3279-3285.
    • (2005) Bioinformatics , vol.21 , pp. 3279-3285
    • Liu, Y.1
  • 35
    • 17444424974 scopus 로고    scopus 로고
    • The structure of alpha-helical coiled coils
    • Lupas,A.N. and Gruber,M. (2005) The structure of alpha-helical coiled coils. Adv. Protein Chem., 70, 37-78.
    • (2005) Adv. Protein Chem , vol.70 , pp. 37-78
    • Lupas, A.N.1    Gruber, M.2
  • 36
    • 23144439591 scopus 로고    scopus 로고
    • BIOVERSE: Enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes
    • McDermott,J. et al. (2005) BIOVERSE: Enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. Nucleic Acids Res., 33, W324-W325.
    • (2005) Nucleic Acids Res , vol.33
    • McDermott, J.1
  • 37
    • 33745605781 scopus 로고    scopus 로고
    • Long-range cooperative binding effects in a T cell receptor variable domain
    • Moza,B. et al. (2006) Long-range cooperative binding effects in a T cell receptor variable domain. Proc. Natl Acad. Sci. USA, 103 9867-9872.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 9867-9872
    • Moza, B.1
  • 38
    • 20444414545 scopus 로고    scopus 로고
    • Linear motifs: Evolutionary interaction switches
    • Neduva,V. and Russell,R. (2005) Linear motifs: Evolutionary interaction switches. FEBS Lett., 579, 3342-3345.
    • (2005) FEBS Lett , vol.579 , pp. 3342-3345
    • Neduva, V.1    Russell, R.2
  • 39
    • 0037250151 scopus 로고    scopus 로고
    • InterDom: A database of putative interacting protein domains for validating predicted protein interactions and complexes
    • Ng,S. et al. (2003) InterDom: A database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res., 31, 251-254.
    • (2003) Nucleic Acids Res , vol.31 , pp. 251-254
    • Ng, S.1
  • 40
    • 16344381315 scopus 로고    scopus 로고
    • Statistical analysis of domains in interacting protein pairs
    • Nye,T. et al. (2004) Statistical analysis of domains in interacting protein pairs. Bioinformatics, 21, 993-1001.
    • (2004) Bioinformatics , vol.21 , pp. 993-1001
    • Nye, T.1
  • 41
    • 22244450719 scopus 로고    scopus 로고
    • Protein families and their evolution-a structural perspective
    • Orengo,C.A. and Thornton,J.M. (2005) Protein families and their evolution-a structural perspective. Annu. Rev. Biochem., 74, 867-900.
    • (2005) Annu. Rev. Biochem , vol.74 , pp. 867-900
    • Orengo, C.A.1    Thornton, J.M.2
  • 42
    • 33645818955 scopus 로고    scopus 로고
    • The DIMA web resource - exploring the protein domain network
    • Pagel,P. et al. (2006) The DIMA web resource - exploring the protein domain network. Bioinformatics, 22, 997-998.
    • (2006) Bioinformatics , vol.22 , pp. 997-998
    • Pagel, P.1
  • 43
    • 38549132879 scopus 로고    scopus 로고
    • DIMA 2.0 - predicted and known domain interactions
    • Pagel,P. et al. (2008) DIMA 2.0 - predicted and known domain interactions. Nucleic Acids Res., 36, D651-D655.
    • (2008) Nucleic Acids Res , vol.36
    • Pagel, P.1
  • 44
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson,T. and Nash,P. (2003) Assembly of cell regulatory systems through protein interaction domains. Science, 300, 445-452.
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 45
    • 10744224197 scopus 로고    scopus 로고
    • Development of human protein reference database as an initial platform for approaching systems biology in humans
    • Peri,S. et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res., 13, 2363-2371.
    • (2003) Genome Res , vol.13 , pp. 2363-2371
    • Peri, S.1
  • 46
    • 0042622252 scopus 로고    scopus 로고
    • ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
    • Puntervoll,P. et al. (2003) ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res., 31, 3625-3630.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3625-3630
    • Puntervoll, P.1
  • 47
    • 34547858473 scopus 로고    scopus 로고
    • Computational analysis of human protein interaction networks
    • Ramfrez,F. et al. (2007) Computational analysis of human protein interaction networks. Proteomics, 7, 2541-2552.
    • (2007) Proteomics , vol.7 , pp. 2541-2552
    • Ramfrez, F.1
  • 48
    • 23444452564 scopus 로고    scopus 로고
    • Probabilistic model of the human protein-protein interaction network
    • Rhodes,D.R. et al. (2005) Probabilistic model of the human protein-protein interaction network. Nat. Biotechnol., 23, 951-959.
    • (2005) Nat. Biotechnol , vol.23 , pp. 951-959
    • Rhodes, D.R.1
  • 49
    • 34548084807 scopus 로고    scopus 로고
    • Inferring protein domain interactions from databases of interacting proteins
    • Riley,R. et al. (2005) Inferring protein domain interactions from databases of interacting proteins. Genome Biol., 6, R89.
    • (2005) Genome Biol , vol.6
    • Riley, R.1
  • 50
    • 38549163153 scopus 로고    scopus 로고
    • CORUM: The comprehensive resource of mammalian protein complexes
    • Ruepp,A. et al. (2007) CORUM: The comprehensive resource of mammalian protein complexes. Nucleic Acids Res., 36, D646-D650.
    • (2007) Nucleic Acids Res , vol.36
    • Ruepp, A.1
  • 51
    • 24944439453 scopus 로고    scopus 로고
    • Methods to reveal domain networks
    • Santonico,E. et al. (2005) Methods to reveal domain networks. Drug Discov. Today, 10, 1111-1117.
    • (2005) Drug Discov. Today , vol.10 , pp. 1111-1117
    • Santonico, E.1
  • 52
    • 33748335463 scopus 로고    scopus 로고
    • A new measure for functional similarity of gene products based on Gene Ontology
    • Schlicker,A. et al. (2006) A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics, 7 302.
    • (2006) BMC Bioinformatics , vol.7 , pp. 302
    • Schlicker, A.1
  • 53
    • 34248576303 scopus 로고    scopus 로고
    • Functional evaluation of domain-domain interactions and human protein interaction networks
    • Schlicker,A. et al. (2007) Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics 23, 859-865.
    • (2007) Bioinformatics , vol.23 , pp. 859-865
    • Schlicker, A.1
  • 54
    • 33745813187 scopus 로고    scopus 로고
    • Reading protein modifications with interaction domains
    • Seet,B.T. et al. (2006) Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol., 7, 473-483.
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , pp. 473-483
    • Seet, B.T.1
  • 55
    • 0035943340 scopus 로고    scopus 로고
    • Correlated sequence-signatures as markers of protein-protein interaction
    • Sprinzak,E. and Margalit,H. (2001) Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol., 311, 681-692.
    • (2001) J. Mol. Biol , vol.311 , pp. 681-692
    • Sprinzak, E.1    Margalit, H.2
  • 56
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: A general repository for interaction datasets
    • Stark,C. et al. (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
    • (2006) Nucleic Acids Res , vol.34
    • Stark, C.1
  • 57
    • 13444257903 scopus 로고    scopus 로고
    • 3did: Interacting protein domains of known three-dimensional structure
    • Stein,A. et al. (2005) 3did: Interacting protein domains of known three-dimensional structure. Nucleic Acids Res., 33, D413-13417.
    • (2005) Nucleic Acids Res , vol.33
    • Stein, A.1
  • 58
    • 13444288174 scopus 로고    scopus 로고
    • E-MSD: An integrated data resource for bioinformatics
    • Velankar,S. et al. (2005) E-MSD: An integrated data resource for bioinformatics. Nucleic Acids Res., 33, D262-D265.
    • (2005) Nucleic Acids Res , vol.33
    • Velankar, S.1
  • 59
    • 41849115573 scopus 로고    scopus 로고
    • InSite: A computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
    • Wang,H. et al. (2007a) InSite: A computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol., 8, R192.
    • (2007) Genome Biol , vol.8
    • Wang, H.1
  • 60
    • 38849149616 scopus 로고    scopus 로고
    • Analysis on multi-domain cooperation for predicting protein-protein interactions
    • Wang,R.S. et al. (2007b) Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformatics, 8 391.
    • (2007) BMC Bioinformatics , vol.8 , pp. 391
    • Wang, R.S.1
  • 61
    • 33746647771 scopus 로고    scopus 로고
    • Topology and weights in a protein domain interaction network - a novel way to predict protein interactions
    • Wuchty,S. (2006) Topology and weights in a protein domain interaction network - a novel way to predict protein interactions. BMC Genomics 7, 122.
    • (2006) BMC Genomics , vol.7 , pp. 122
    • Wuchty, S.1


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