메뉴 건너뛰기




Volumn 40, Issue D1, 2012, Pages

Minimotif Miner 3.0: Database expansion and significantly improved reduction of false-positive predictions from consensus sequences

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CONSENSUS SEQUENCE; FALSE POSITIVE RESULT; INTERNET; LINEAR REGRESSION ANALYSIS; MINIMOTIF MINER DATABASE 3.0; ONLINE SYSTEM; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN MOTIF;

EID: 84859219888     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1189     Document Type: Article
Times cited : (53)

References (51)
  • 2
    • 77954267294 scopus 로고    scopus 로고
    • SLiMFinder: A web server to find novel, significantly over-represented, short protein motifs
    • Davey,N.E., Haslam,N.J., Shields,D.C. and Edwards,R.J. (2010) SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res., 38, W534-W549.
    • (2010) Nucleic Acids Res. , vol.38
    • Davey, N.E.1    Haslam, N.J.2    Shields, D.C.3    Edwards, R.J.4
  • 3
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signalling interactions using short sequence motifs
    • DOI 10.1093/nar/gkg584
    • Obenauer,J.C., Cantley,L.C. and Yaffe,M.B. (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res., 31, 3635-3641. (Pubitemid 37442212)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 8
  • 10
    • 80053913061 scopus 로고    scopus 로고
    • DomPep-A general method for predicting modular domain-mediated protein-protein interactions
    • Li,L., Zhao,B., Du,J., Zhang,K., Ling,C.X. and Li,S.S.-C. (2011) DomPep-A general method for predicting modular domain-mediated protein-protein interactions. PLoS One, 6, e25528.
    • (2011) PLoS One , vol.6
    • Li, L.1    Zhao, B.2    Du, J.3    Zhang, K.4    Ling, C.X.5    Li, S.S.-C.6
  • 11
    • 78649789086 scopus 로고    scopus 로고
    • A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions
    • Rajasekaran,S., Merlin,J.C., Kundeti,V., Mi,T., Oommen,A., Vyas,J., Alaniz,I., Chung,K., Chowdhury,F., Deverasatty,S. et al. (2010) A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. Proteins, 79, 153-164.
    • (2010) Proteins , vol.79 , pp. 153-164
    • Rajasekaran, S.1    Merlin, J.C.2    Kundeti, V.3    Mi, T.4    Oommen, A.5    Vyas, J.6    Alaniz, I.7    Chung, K.8    Chowdhury, F.9    Deverasatty, S.10
  • 14
    • 78651344377 scopus 로고    scopus 로고
    • 3did: Identification and classification of domain-based interactions of known three-dimensional structure
    • Stein,A., Céol,A. and Aloy,P. (2011) 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res., 39, D718-D723.
    • (2011) Nucleic Acids Res. , vol.39
    • Stein, A.1    Céol, A.2    Aloy, P.3
  • 16
    • 75849126506 scopus 로고    scopus 로고
    • The structural basis of peptide-protein binding strategies
    • London,N., Movshovitz-Attias,D. and Schueler-Furman,O. (2010) The structural basis of peptide-protein binding strategies. Structure, 18, 188-199.
    • (2010) Structure , vol.18 , pp. 188-199
    • London, N.1    Movshovitz-Attias, D.2    Schueler-Furman, O.3
  • 17
    • 2942598149 scopus 로고    scopus 로고
    • PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
    • DOI 10.1002/pmic.200300772
    • Hornbeck,P.V., Chabra,I., Kornhauser,J.M., Skrzypek,E. and Zhang,B. (2004) PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics, 4, 1551-1561. (Pubitemid 38738314)
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1551-1561
    • Hornbeck, P.V.1    Chabra, I.2    Kornhauser, J.M.3    Skrzypek, E.4    Zhang, B.5
  • 20
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010.
    • The Universal Protein Resource (UniProt) in 2010. (2010) Nucleic Acids Res., 38, D142-D148.
    • (2010) Nucleic Acids Res. , vol.38
  • 23
    • 78650821937 scopus 로고    scopus 로고
    • Large-scale discovery and characterization of protein regulatory motifs in eukaryotes
    • Lieber,D.S., Elemento,O. and Tavazoie,S. (2010) Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One, 5, e14444.
    • (2010) PLoS One , vol.5
    • Lieber, D.S.1    Elemento, O.2    Tavazoie, S.3
  • 24
    • 52049111184 scopus 로고    scopus 로고
    • Viral infection and human disease- insights from minimotifs
    • Kadaveru,K., Vyas,J. and Schiller,M.R. (2008) Viral infection and human disease- insights from minimotifs. Front Biosci., 13, 6455-6471.
    • (2008) Front Biosci. , vol.13 , pp. 6455-6471
    • Kadaveru, K.1    Vyas, J.2    Schiller, M.R.3
  • 26
    • 67949109561 scopus 로고    scopus 로고
    • Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs
    • Evans,P., Dampier,W., Ungar,L. and Tozeren,A. (2009) Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. BMC Med. Genomics, 2, 27.
    • (2009) BMC Med. Genomics , vol.2 , pp. 27
    • Evans, P.1    Dampier, W.2    Ungar, L.3    Tozeren, A.4
  • 27
    • 52049111184 scopus 로고    scopus 로고
    • Viral infection and human disease - Insights from minimotifs
    • Kadaveru,K., Vyas,J. and Schiller,M.R. (2008) Viral infection and human disease - insights from minimotifs. Front. Biosci., 13, 6455-6471.
    • (2008) Front. Biosci. , vol.13 , pp. 6455-6471
    • Kadaveru, K.1    Vyas, J.2    Schiller, M.R.3
  • 28
    • 56449096489 scopus 로고    scopus 로고
    • Approved drug mimics of short peptide ligands from protein interaction motifs
    • Parthasarathi,L., Casey,F., Stein,A., Aloy,P. and Shields,D.C. (2008) Approved drug mimics of short peptide ligands from protein interaction motifs. J. Chem. Inf. Model., 48, 1943-1948.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1943-1948
    • Parthasarathi, L.1    Casey, F.2    Stein, A.3    Aloy, P.4    Shields, D.C.5
  • 35
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios,I., Salwínski,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. (Pubitemid 34679570)
    • (2002) Nucleic Acids Research , vol.30 , Issue.1 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.-M.5    Eisenberg, D.6
  • 38
    • 75849158230 scopus 로고    scopus 로고
    • The Gene Ontology in 2010: Extensions and refinements
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res., 38, D331-D335.
    • (2010) Nucleic Acids Res. , vol.38
  • 42
    • 0031572847 scopus 로고    scopus 로고
    • The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling
    • Arold,S., Franken,P., Strub,M.P., Hoh,F., Benichou,S., Benarous,R. and Dumas,C. (1997) The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Structure, 5, 1361-1372. (Pubitemid 27484477)
    • (1997) Structure , vol.5 , Issue.10 , pp. 1361-1372
    • Arold, S.1    Franken, P.2    Strub, M.-P.3    Hoh, F.4    Benichou, S.5    Benarous, R.6    Dumas, C.7
  • 43
    • 38349109364 scopus 로고    scopus 로고
    • A diacidic motif in human immunodeficiency virus type 1 Nef is a novel determinant of binding to AP-2
    • Lindwasser,O.W., Smith,W.J., Chaudhuri,R., Yang,P., Hurley,J.H. and Bonifacino,J.S. (2008) A diacidic motif in human immunodeficiency virus type 1 Nef is a novel determinant of binding to AP-2. J. Virol., 82, 1166-1174.
    • (2008) J. Virol. , vol.82 , pp. 1166-1174
    • Lindwasser, O.W.1    Smith, W.J.2    Chaudhuri, R.3    Yang, P.4    Hurley, J.H.5    Bonifacino, J.S.6
  • 44
    • 32444451769 scopus 로고    scopus 로고
    • Modulation of cellular protein trafficking by human immunodeficiency virus type 1 Nef: Role of the acidic residue in the ExxxLL motif
    • DOI 10.1128/JVI.80.4.1837-1849.2006
    • Coleman,S.H., Madrid,R., Van Damme,N., Mitchell,R.S., Bouchet,J., Servant,C., Pillai,S., Benichou,S. and Guatelli,J.C. (2006) Modulation of cellular protein trafficking by human immunodeficiency virus type 1 Nef: role of the acidic residue in the ExxxLL motif. J. Virol., 80, 1837-1849. (Pubitemid 43228724)
    • (2006) Journal of Virology , vol.80 , Issue.4 , pp. 1837-1849
    • Coleman, S.H.1    Madrid, R.2    Van Damme, N.3    Mitchell, R.S.4    Bouchet, J.5    Servant, C.6    Pillai, S.7    Benichou, S.8    Guatelli, J.C.9
  • 45
    • 0032488055 scopus 로고    scopus 로고
    • A dileucine motif in HIV-1 Nef is essential for sorting into clathrin-coated pits and for downregulation of CD4
    • Greenberg,M., DeTulleo,L., Rapoport,I., Skowronski,J. and Kirchhausen,T. (1998) A dileucine motif in HIV-1 Nef is essential for sorting into clathrin-coated pits and for downregulation of CD4. Curr. Biol., 8, 1239-1242. (Pubitemid 29006666)
    • (1998) Current Biology , vol.8 , Issue.22 , pp. 1239-1242
    • Greenberg, M.1    DeTulleo, L.2    Rapoport, I.3    Skowronski, J.4    Kirchhausen, T.5
  • 46
    • 13444291133 scopus 로고    scopus 로고
    • Leucine-specific, functional interactions between human immunodeficiency virus type 1 Nef and adaptor protein complexes
    • DOI 10.1128/JVI.79.4.2066-2078.2005
    • Coleman,S.H., Van Damme,N., Day,J.R., Noviello,C.M., Hitchin,D., Madrid,R., Benichou,S. and Guatelli,J.C. (2005) Leucine-specific, functional interactions between human immunodeficiency virus type 1 Nef and adaptor protein complexes. J. Virol., 79, 2066-2078. (Pubitemid 40204564)
    • (2005) Journal of Virology , vol.79 , Issue.4 , pp. 2066-2078
    • Coleman, S.H.1    Van Damme, N.2    Day, J.R.3    Noviello, C.M.4    Hitchin, D.5    Madrid, R.6    Benichou, S.7    Guatelli, J.C.8
  • 47
    • 0028361644 scopus 로고
    • Regulation of human immunodeficiency virus Nef protein by phosphorylation
    • DOI 10.1006/viro.1994.1278
    • Bandres,J.C., Luria,S. and Ratner,L. (1994) Regulation of human immunodeficiency virus Nef protein by phosphorylation. Virology, 201, 157-161. (Pubitemid 24165598)
    • (1994) Virology , vol.201 , Issue.1 , pp. 157-161
    • Bandres, J.O.1    Luria, S.2    Ratner, L.3
  • 48
    • 0029021821 scopus 로고
    • In vitro binding and phosphorylation of human immunodeficiency virus type 1 Nef protein by serine/threonine protein kinase
    • Bodéus,M., Marie-Cardine,A., Bougeret,C., Ramos-Morales,F. and Benarous,R. (1995) In vitro binding and phosphorylation of human immunodeficiency virus type 1 Nef protein by serine/threonine protein kinase. J. Gen. Virol., 76(Pt 6), 1337-1344.
    • (1995) J. Gen. Virol. , vol.76 , Issue.PART 6 , pp. 1337-1344
    • Bodéus, M.1    Marie-Cardine, A.2    Bougeret, C.3    Ramos-Morales, F.4    Benarous, R.5
  • 49
    • 0028968962 scopus 로고
    • The human immunodeficiency virus type 1 Nef protein functions as a protein kinase C substrate in vitro
    • Coates,K. and Harris,M. (1995) The human immunodeficiency virus type 1 Nef protein functions as a protein kinase C substrate in vitro. J. Gen. Virol, 76(Pt 4), 837-844.
    • (1995) J. Gen. Virol , vol.76 , Issue.PART 4 , pp. 837-844
    • Coates, K.1    Harris, M.2
  • 50
    • 84862159708 scopus 로고    scopus 로고
    • Minimotif Miner: A computation tool to investigate protein function, disease, and genetic diversity
    • Coligan,J.E., Dunn,B.M., Speicher,D.W. and Winkler,H. (eds), John Wiley & Sons, Inc., New York
    • Schiller,M.R. (2007) Minimotif Miner: a computation tool to investigate protein function, disease, and genetic diversity. In: Coligan,J.E., Dunn,B.M., Speicher,D.W. and Winkler,H. (eds), Current Protocols in Protein Science. John Wiley & Sons, Inc., New York, pp. 2.12.1-2.12.14.
    • (2007) Current Protocols in Protein Science
    • Schiller, M.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.