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Volumn 72, Issue 1, 2008, Pages 461-473

Protein domain annotation with integration of heterogeneous information sources

Author keywords

Domain coexisting features; Domain function prediction; Predicted domain domain interactions; Protein domain mapping; Statistical model; Support vector machines

Indexed keywords

ACCURACY; ARTICLE; DATA ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; RELIABILITY; STATISTICAL MODEL; SUPPORT VECTOR MACHINE;

EID: 44949143041     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21943     Document Type: Article
Times cited : (18)

References (29)
  • 1
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domain-domain interactions from protein-protein interactions
    • Deng M, Mehta S, Sun F, Chen T. Inferring domain-domain interactions from protein-protein interactions. Genome Res 2002;12(10):1540-1548.
    • (2002) Genome Res , vol.12 , Issue.10 , pp. 1540-1548
    • Deng, M.1    Mehta, S.2    Sun, F.3    Chen, T.4
  • 2
    • 33745327144 scopus 로고    scopus 로고
    • An integrated approach to the prediction of domain-domain interactions
    • Lee H, Deng M, Sun F, Chen T. An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics 2006;7:269.
    • (2006) BMC Bioinformatics , vol.7 , pp. 269
    • Lee, H.1    Deng, M.2    Sun, F.3    Chen, T.4
  • 3
    • 34548084807 scopus 로고    scopus 로고
    • Inferring protein domain interactions from databases of interacting proteins
    • Riley R, Lee C, Sabatti C, Eisenberg D. Inferring protein domain interactions from databases of interacting proteins. Genome Biol 2005;6(10):R89.
    • (2005) Genome Biol , vol.6 , Issue.10
    • Riley, R.1    Lee, C.2    Sabatti, C.3    Eisenberg, D.4
  • 4
    • 33644835242 scopus 로고    scopus 로고
    • Inferring protein interactions from experimental data by association probabilistic method
    • Chen L, Wu LY, Wang Y, Zhang XS. Inferring protein interactions from experimental data by association probabilistic method. Proteins 2006;62:833-837.
    • (2006) Proteins , vol.62 , pp. 833-837
    • Chen, L.1    Wu, L.Y.2    Wang, Y.3    Zhang, X.S.4
  • 5
    • 0037138386 scopus 로고    scopus 로고
    • Protein domain analysis in the era of complete genomes
    • Copley RR, Doerks T, Letunic I, Bork P. Protein domain analysis in the era of complete genomes. FEBS Lett 2002;513(1):129-134.
    • (2002) FEBS Lett , vol.513 , Issue.1 , pp. 129-134
    • Copley, R.R.1    Doerks, T.2    Letunic, I.3    Bork, P.4
  • 6
    • 0034674175 scopus 로고    scopus 로고
    • Estimating the number of protein folds and families from complete genome data
    • Wolf YI, Grishin NV, Koonin EV. Estimating the number of protein folds and families from complete genome data, J Mol Biol 2000;299(4):897-905.
    • (2000) J Mol Biol , vol.299 , Issue.4 , pp. 897-905
    • Wolf, Y.I.1    Grishin, N.V.2    Koonin, E.V.3
  • 7
    • 0027122748 scopus 로고
    • One thousand families for the molecular biologist
    • Chothia C. One thousand families for the molecular biologist. Nature 1992;357:543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 9
    • 13244260791 scopus 로고    scopus 로고
    • Automatic annotation of protein motif function with gene ontology terms
    • Lu X, Zhai C, Gopalakrishnan V, Buchanan BG. Automatic annotation of protein motif function with gene ontology terms. BMC Bioinformatics 2004;5:122.
    • (2004) BMC Bioinformatics , vol.5 , pp. 122
    • Lu, X.1    Zhai, C.2    Gopalakrishnan, V.3    Buchanan, B.G.4
  • 11
    • 0033957841 scopus 로고    scopus 로고
    • ProDom and ProDomCG: Tools for protein domain analysis and whole genome comparisons
    • Corpet F, Servant F, Gouzy J, Kahn D. ProDom and ProDomCG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res 2000;28(1):267-269.
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 267-269
    • Corpet, F.1    Servant, F.2    Gouzy, J.3    Kahn, D.4
  • 13
    • 0035816218 scopus 로고    scopus 로고
    • Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    • Apic G, Gough J, Teichmann SA. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 2001;310:311-325.
    • (2001) J Mol Biol , vol.310 , pp. 311-325
    • Apic, G.1    Gough, J.2    Teichmann, S.A.3
  • 14
    • 33750951499 scopus 로고    scopus 로고
    • Global phylogeny determined by the combination of protein daomains in proteoms
    • Wang M, Caetano-Anolles G. Global phylogeny determined by the combination of protein daomains in proteoms. Mol Boi Evol 2006;23(12):2444-2454.
    • (2006) Mol Boi Evol , vol.23 , Issue.12 , pp. 2444-2454
    • Wang, M.1    Caetano-Anolles, G.2
  • 15
    • 38849149616 scopus 로고    scopus 로고
    • Analysis on multi-domain cooperation for predicting protein-protein interactions
    • Wang RS, Wang Y, Wu L-Y, Zhang X-S, Chen LN. Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformatics 2007;8:391.
    • (2007) BMC Bioinformatics , vol.8 , pp. 391
    • Wang, R.S.1    Wang, Y.2    Wu, L.-Y.3    Zhang, X.-S.4    Chen, L.N.5
  • 16
    • 0035232163 scopus 로고    scopus 로고
    • An insight into domain combination
    • Apic G, Gough J, Teichmann SA. An insight into domain combination. Bioinformatics 2001;17(Suppl 1):S83-S89.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Apic, G.1    Gough, J.2    Teichmann, S.A.3
  • 17
    • 0036307754 scopus 로고    scopus 로고
    • The geometry of domain combinations in proteins
    • Bashton M, Chothia C. The geometry of domain combinations in proteins. J Mol Biol 2002;315:927-939.
    • (2002) J Mol Biol , vol.315 , pp. 927-939
    • Bashton, M.1    Chothia, C.2
  • 19
    • 13444282474 scopus 로고    scopus 로고
    • Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH. InterPro, progress and status in 2005. Nucleic Acids Res 2005;33 (Database Issue):D201-D205.
    • Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH. InterPro, progress and status in 2005. Nucleic Acids Res 2005;33 (Database Issue):D201-D205.
  • 22
    • 0029916911 scopus 로고    scopus 로고
    • The Swiss-Prot protein sequence data bank and its new supplement TREMBL
    • Bairoch A, Apweiler R. The Swiss-Prot protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res 1996;24:21-25.
    • (1996) Nucleic Acids Res , vol.24 , pp. 21-25
    • Bairoch, A.1    Apweiler, R.2
  • 24
    • 13844264506 scopus 로고    scopus 로고
    • iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    • Finn RD, Marshall M, Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 2005;21:410-412.
    • (2005) Bioinformatics , vol.21 , pp. 410-412
    • Finn, R.D.1    Marshall, M.2    Bateman, A.3
  • 25
    • 29144442904 scopus 로고    scopus 로고
    • Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
    • Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 2005;21:i302-i310.
    • (2005) Bioinformatics , vol.21
    • Nabieva, E.1    Jim, K.2    Agarwal, A.3    Chazelle, B.4    Singh, M.5
  • 26
    • 33745619564 scopus 로고    scopus 로고
    • Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    • Chua HN, Sung WK, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006;22:1623-1630.
    • (2006) Bioinformatics , vol.22 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.K.2    Wong, L.3
  • 27
    • 44949248411 scopus 로고    scopus 로고
    • Protein classification with imbalanced data
    • in press
    • Zhao X, Chen LN, Aihara K. Protein classification with imbalanced data. PROTEINS, in press.
    • PROTEINS
    • Zhao, X.1    Chen, L.N.2    Aihara, K.3
  • 28
    • 0036790999 scopus 로고    scopus 로고
    • From the Cover: Transitive functional annotation by shortest-path analysis of gene expression data
    • Zhou X, Kao MCJ, Wong WH. From the Cover: Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci USA 2002;99:12783-12788.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 12783-12788
    • Zhou, X.1    Kao, M.C.J.2    Wong, W.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.