메뉴 건너뛰기




Volumn 28, Issue 4, 2004, Pages 291-301

Predicting protein-protein interactions by a supervised learning classifier

Author keywords

Genome analysis; Protein domains; Protein protein interactions; SVM learning

Indexed keywords

BIOTECHNOLOGY; CELL CULTURE; GENES; MOLECULAR BIOLOGY; OPTIMIZATION; PARAMETER ESTIMATION; PROBLEM SOLVING;

EID: 9544257312     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2004.07.003     Document Type: Article
Times cited : (6)

References (49)
  • 1
    • 0041669372 scopus 로고    scopus 로고
    • The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair
    • Acharya, S., Foster, P.L., Brooks, P., Fishel, R., 2003. The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair. Mol. Cell. 12, 233-246.
    • (2003) Mol. Cell. , vol.12 , pp. 233-246
    • Acharya, S.1    Foster, P.L.2    Brooks, P.3    Fishel, R.4
  • 4
    • 0029127222 scopus 로고
    • A variety of DNA-binding and multimeric proteins contain the histone fold motif
    • Baxevanis, A.D., Arents, G., Moudrianakis, E.N., Landsman, D., 1995. A variety of DNA-binding and multimeric proteins contain the histone fold motif. Nucl. Acids Res. 23, 2685-2691.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 2685-2691
    • Baxevanis, A.D.1    Arents, G.2    Moudrianakis, E.N.3    Landsman, D.4
  • 6
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • Bock, J.R., Gough, D.A., 2001. Predicting protein-protein interactions from primary structure. Bioinformatics 17, 455-460.
    • (2001) Bioinformatics , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 7
    • 27144489164 scopus 로고    scopus 로고
    • A tutorial on support vector machines for pattern recognition
    • Burges, C.J.C., 1998. A tutorial on support vector machines for pattern recognition. Data Mining and Knowledge Discovery 2, 121-167.
    • (1998) Data Mining and Knowledge Discovery , vol.2 , pp. 121-167
    • Burges, C.J.C.1
  • 8
    • 0038268182 scopus 로고    scopus 로고
    • Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA: Crystal structure of an oligomeric complex of yeast SmF
    • Collins, B.M., Cubeddu, L., Naidoo, N., Harrop, S.J., Kornfeld, G.D., Dawes, I.W., Curmi, P.M., Mabbutt, B.C., 2003. Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA: crystal structure of an oligomeric complex of yeast SmF. J. Biol. Chem. 278, 17291-17298.
    • (2003) J. Biol. Chem. , vol.278 , pp. 17291-17298
    • Collins, B.M.1    Cubeddu, L.2    Naidoo, N.3    Harrop, S.J.4    Kornfeld, G.D.5    Dawes, I.W.6    Curmi, P.M.7    Mabbutt, B.C.8
  • 10
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar, T., Snel, B., Huynen, M., Bork, P., 1998. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324-328.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 11
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • Deane, C.M., Salwinski, L., Xenarios, I., Eisenberg, D., 2002. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell Proteomics 1, 349-356.
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 349-356
    • Deane, C.M.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 12
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domain-domain interactions from protein-protein interactions
    • Deng, M., Mehta, S., Sun, F., Chen, T., 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    Mehta, S.2    Sun, F.3    Chen, T.4
  • 13
    • 0032478545 scopus 로고    scopus 로고
    • Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT
    • Ditzel, L., Lowe, J., Stock, D., Stetter, K.O., Huber, H., Huber, R., Steinbacher, S., 1998. Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Cell 93, 125-138.
    • (1998) Cell , vol.93 , pp. 125-138
    • Ditzel, L.1    Lowe, J.2    Stock, D.3    Stetter, K.O.4    Huber, H.5    Huber, R.6    Steinbacher, S.7
  • 16
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright, A.J., Iliopoulos, I., Kyrpides, N.C., Ouzounis, C.A., 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    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 19
    • 0035672003 scopus 로고    scopus 로고
    • Probabilistic prediction of unknown metabolic and signal-transduction networks
    • Gomez, S.M., Lo, S.H., Rzhetsky, A., 2001. Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics 159, 1291-1298.
    • (2001) Genetics , vol.159 , pp. 1291-1298
    • Gomez, S.M.1    Lo, S.H.2    Rzhetsky, A.3
  • 20
    • 9544233969 scopus 로고    scopus 로고
    • Semiparametric estimation of stochastic frontiers: A Bayesian penalized approach
    • School of Economics, University of Queensland, Australia
    • Hajargasht, G., 2003. Semiparametric estimation of stochastic frontiers: a Bayesian penalized approach. CEPA Working Papers Series WP04. School of Economics, University of Queensland, Australia.
    • (2003) CEPA Working Papers Series , vol.WP04
    • Hajargasht, G.1
  • 22
    • 0036158552 scopus 로고    scopus 로고
    • A simple decomposition method for support vector machines
    • Hsu, C.-W., Lin, C.-J., 2002. A simple decomposition method for support vector machines. Machine Learning 46, 291-314.
    • (2002) Machine Learning , vol.46 , pp. 291-314
    • Hsu, C.-W.1    Lin, C.-J.2
  • 23
    • 0010656061 scopus 로고    scopus 로고
    • Exploring the protein interactome using comprehensive two-hybrid projects
    • Ito, T., Chiba, T., Yoshida, M., 2001. Exploring the protein interactome using comprehensive two-hybrid projects. Trends Biotechnol. 19, S23-S27.
    • (2001) Trends Biotechnol. , vol.19
    • Ito, T.1    Chiba, T.2    Yoshida, M.3
  • 25
    • 0642343787 scopus 로고    scopus 로고
    • Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair
    • Kim, W.K., Park, J., Suh, J.K., 2002. Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. Genome Informatics 13, 42-50.
    • (2002) Genome Informatics , vol.13 , pp. 42-50
    • Kim, W.K.1    Park, J.2    Suh, J.K.3
  • 26
    • 0035369531 scopus 로고    scopus 로고
    • Protein-protein interaction maps: A lead towards cellular functions
    • Legrain, P., Wojcik, J., Gauthier, J.M., 2001. Protein-protein interaction maps: a lead towards cellular functions. Trends Genet. 17, 346-352.
    • (2001) Trends Genet. , vol.17 , pp. 346-352
    • Legrain, P.1    Wojcik, J.2    Gauthier, J.M.3
  • 29
    • 35248846436 scopus 로고    scopus 로고
    • Detecting hidden messages using higher-order statistics and support vector machines
    • Petitcolas, F.A.P. (Ed.), The Fifth International Workshop on Information Hiding. Springer-Verlag
    • Lyu, S., Farid, H., 2002. Detecting hidden messages using higher-order statistics and support vector machines. In: Petitcolas, F.A.P. (Ed.), The Fifth International Workshop on Information Hiding. Lecture Notes in Computer Science 2578. Springer-Verlag.
    • (2002) Lecture Notes in Computer Science , vol.2578
    • Lyu, S.1    Farid, H.2
  • 33
    • 0038620469 scopus 로고    scopus 로고
    • Integrative approach for computationally inferring protein domain interactions
    • Ng, S.K., Zhang, Z., Tan, S.H., 2003. Integrative approach for computationally inferring protein domain interactions. Bioinformatics 19, 923-929.
    • (2003) Bioinformatics , vol.19 , pp. 923-929
    • Ng, S.K.1    Zhang, Z.2    Tan, S.H.3
  • 34
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren, I.M., Thornton, J.M., 2003. Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol. 325, 991-1018.
    • (2003) J. Mol. Biol. , vol.325 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 36
    • 0036083294 scopus 로고    scopus 로고
    • Extraction of knowledge on protein-protein interaction by association rule discovery
    • Oyama, T., Kitano, K., Satou, K., Ito, T., 2002. Extraction of knowledge on protein-protein interaction by association rule discovery. Bioinformatics 18, 705-714.
    • (2002) Bioinformatics , vol.18 , pp. 705-714
    • Oyama, T.1    Kitano, K.2    Satou, K.3    Ito, T.4
  • 37
    • 0035983515 scopus 로고    scopus 로고
    • Crystal structure of the CCTgamma apical domain: Implications for substrate binding to the eukaryotic cytosolic chaperonin
    • Pappenberger, G., Wilsher, J.A., Roe, S.M., Counsell, D.J., Willison, K.R., Pearl, L.H., 2002. Crystal structure of the CCTgamma apical domain: implications for substrate binding to the eukaryotic cytosolic chaperonin. J. Mol. Biol. 318, 1367-1379.
    • (2002) J. Mol. Biol. , vol.318 , pp. 1367-1379
    • Pappenberger, G.1    Wilsher, J.A.2    Roe, S.M.3    Counsell, D.J.4    Willison, K.R.5    Pearl, L.H.6
  • 38
    • 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., 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
  • 39
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson, T, 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
  • 40
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • Pazos, F., 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
  • 42
    • 0038438514 scopus 로고    scopus 로고
    • IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    • Schaffer, A.A., Wolf, Y.I., Ponting, C.P., Koonin, E.V., Aravind, L., Altschul, S.F., 1999. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 15, 1000-1011.
    • (1999) Bioinformatics , vol.15 , pp. 1000-1011
    • Schaffer, A.A.1    Wolf, Y.I.2    Ponting, C.P.3    Koonin, E.V.4    Aravind, L.5    Altschul, S.F.6
  • 43
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski, B., Uetz, P., Fields, S., 2000. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18, 1257-1261.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 44
    • 0035943340 scopus 로고    scopus 로고
    • Correlated sequence-signatures as markers of protein-protein interaction
    • Sprinzak, E., 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
  • 46
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., Bork, P., 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 47
    • 1842861590 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
    • Wodak, S.J., Mendez, R., 2004. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr. Opin. Struct. Biol. 14, 242-249.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 242-249
    • Wodak, S.J.1    Mendez, R.2
  • 48
    • 0035224503 scopus 로고    scopus 로고
    • Protein-protein interaction map inference using interacting domain profile pairs
    • Wojcik, J., Schachter, V., 2001. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 17 (Suppl. 1), S296-S305.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Wojcik, J.1    Schachter, V.2
  • 49
    • 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., Eisenberg, D., 2002. DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 30, 303-305.
    • (2002) Nucl. 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.