메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

Author keywords

[No Author keywords available]

Indexed keywords

DOMAIN-DOMAIN INTERACTIONS; EXPERIMENTAL METHODS; INTERACTION PREDICTION; INTERACTION PROFILES; LEAVE-ONE-OUT CROSS VALIDATIONS; PROTEIN-PROTEIN INTERACTIONS; STRUCTURAL INFORMATION; SUPPORT VECTOR MACHINE (SVMS);

EID: 77958554380     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-537     Document Type: Article
Times cited : (19)

References (38)
  • 2
    • 34248371273 scopus 로고    scopus 로고
    • Predicting protein-protein interactions based only on sequences information
    • 10.1073/pnas.0607879104, 1838603, 17360525
    • Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci USA 2007, 104:4337-4341. 10.1073/pnas.0607879104, 1838603, 17360525.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 4337-4341
    • Shen, J.1    Zhang, J.2    Luo, X.3    Zhu, W.4    Yu, K.5    Chen, K.6    Li, Y.7    Jiang, H.8
  • 3
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • 10.1093/bioinformatics/17.5.455, 11331240
    • Bock JR, Gough DA. Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17:455-460. 10.1093/bioinformatics/17.5.455, 11331240.
    • (2001) Bioinformatics , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 4
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • 10.1126/science.285.5428.751, 10427000
    • Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285:751-753. 10.1126/science.285.5428.751, 10427000.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 7
    • 20844454090 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
    • 10.1093/bioinformatics/bti443, 15855251
    • Selim Aytuna A, Gursoy A, Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 2005, 21:2850-2855. 10.1093/bioinformatics/bti443, 15855251.
    • (2005) Bioinformatics , vol.21 , pp. 2850-2855
    • Selim Aytuna, A.1    Gursoy, A.2    Keskin, O.3
  • 8
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • 10.1093/protein/14.9.609, 11707606
    • Pazos F, Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering 2001, 14:609-614. 10.1093/protein/14.9.609, 11707606.
    • (2001) Protein Engineering , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 9
    • 0034595516 scopus 로고    scopus 로고
    • Co-evolution of proteins with their interaction partners
    • 10.1006/jmbi.2000.3732, 10860738
    • Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. Co-evolution of proteins with their interaction partners. J Mol Biol 2000, 299:283-293. 10.1006/jmbi.2000.3732, 10860738.
    • (2000) J Mol Biol , vol.299 , pp. 283-293
    • Goh, C.S.1    Bogan, A.A.2    Joachimiak, M.3    Walther, D.4    Cohen, F.E.5
  • 10
    • 0036435908 scopus 로고    scopus 로고
    • Co-evolutionary analysis reveals insights into protein-protein interactions
    • 10.1016/S0022-2836(02)01038-0, 12421567
    • Goh CS, Cohen FE. Co-evolutionary analysis reveals insights into protein-protein interactions. J Mol Biol 2002, 324:177-192. 10.1016/S0022-2836(02)01038-0, 12421567.
    • (2002) J Mol Biol , vol.324 , pp. 177-192
    • Goh, C.S.1    Cohen, F.E.2
  • 11
    • 25144479967 scopus 로고    scopus 로고
    • Inferring protein-protein interactions through high-throughput interaction data from diverse organisms
    • 10.1093/bioinformatics/bti492, 15905281
    • Liu Y, Liu N, Zhao H. Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics 2005, 21:3279-3285. 10.1093/bioinformatics/bti492, 15905281.
    • (2005) Bioinformatics , vol.21 , pp. 3279-3285
    • Liu, Y.1    Liu, N.2    Zhao, H.3
  • 12
    • 33846868175 scopus 로고    scopus 로고
    • Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
    • 1781468, 17212819
    • Craig RA, Liao L. Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices. BMC Bioinformatics 2007, 8(6). 1781468, 17212819.
    • (2007) BMC Bioinformatics , vol.8 , Issue.6
    • Craig, R.A.1    Liao, L.2
  • 13
    • 34249730066 scopus 로고    scopus 로고
    • Evolutionary conservation of domain-domain interactions
    • 1794438, 17184549, R125
    • Itzhaki Z, Akiva E, Altuvia Y, Margalit H. Evolutionary conservation of domain-domain interactions. Genome Biology 2006, 7(R125). 1794438, 17184549.
    • (2006) Genome Biology , vol.7
    • Itzhaki, Z.1    Akiva, E.2    Altuvia, Y.3    Margalit, H.4
  • 14
    • 55749093288 scopus 로고    scopus 로고
    • Physical protein-protein interactions predicted from microarrays
    • 10.1093/bioinformatics/btn498, 2579715, 18829707
    • Soong T, Wrzeszczynski KO, Rost B. Physical protein-protein interactions predicted from microarrays. Bioinformatics 2008, 24:2608-2614. 10.1093/bioinformatics/btn498, 2579715, 18829707.
    • (2008) Bioinformatics , vol.24 , pp. 2608-2614
    • Soong, T.1    Wrzeszczynski, K.O.2    Rost, B.3
  • 15
    • 33645319955 scopus 로고    scopus 로고
    • Predicting interactions in protein networks by completing defective cliques
    • 10.1093/bioinformatics/btl014, 16455753
    • Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics 2006, 22:823-829. 10.1093/bioinformatics/btl014, 16455753.
    • (2006) Bioinformatics , vol.22 , pp. 823-829
    • Yu, H.1    Paccanaro, A.2    Trifonov, V.3    Gerstein, M.4
  • 16
    • 24744435534 scopus 로고    scopus 로고
    • Kernel methods for predicting protein-protein interactions
    • 10.1093/bioinformatics/bti1016, 15961482
    • Ben-Hur A, Stafford Noble W. Kernel methods for predicting protein-protein interactions. Bioinformatics 2005, 21:i38-i46. 10.1093/bioinformatics/bti1016, 15961482.
    • (2005) Bioinformatics , vol.21
    • Ben-Hur, A.1    Stafford Noble, W.2
  • 17
    • 0035224503 scopus 로고    scopus 로고
    • Protein-protein interaction map inference using interacting domain profile pairs
    • Wojcik J, Schachter V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 2001, 17:S296-S305.
    • (2001) Bioinformatics , vol.17
    • Wojcik, J.1    Schachter, V.2
  • 18
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domain-domain interactions from protein-protein interactions
    • 10.1101/gr.153002, 187530, 12368246
    • Deng M, Mehta S, Sun F, Chen T. Inferring domain-domain interactions from protein-protein interactions. Genome Research 2002, 12:1540-1548. 10.1101/gr.153002, 187530, 12368246.
    • (2002) Genome Research , vol.12 , pp. 1540-1548
    • Deng, M.1    Mehta, S.2    Sun, F.3    Chen, T.4
  • 19
    • 33745327144 scopus 로고    scopus 로고
    • An integrated approach to the prediction of domain-domain interactions
    • 10.1186/1471-2105-7-269, 1481624, 16725050
    • Lee H, Deng M, Sun F, Chen T. An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics 2006, 7:269. 10.1186/1471-2105-7-269, 1481624, 16725050.
    • (2006) BMC Bioinformatics , vol.7 , pp. 269
    • Lee, H.1    Deng, M.2    Sun, F.3    Chen, T.4
  • 20
    • 0037250151 scopus 로고    scopus 로고
    • InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
    • 10.1093/nar/gkg079, 165526, 12519994
    • Ng SK, Zhang Z, Tan SH, Lin K. InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Research 2003, 31:251-254. 10.1093/nar/gkg079, 165526, 12519994.
    • (2003) Nucleic Acids Research , vol.31 , pp. 251-254
    • Ng, S.K.1    Zhang, Z.2    Tan, S.H.3    Lin, K.4
  • 21
    • 33847753484 scopus 로고    scopus 로고
    • Predicting domain-domain interactions using a parsimony approach
    • 10.1186/gb-2006-7-11-r104, 1794579, 17094802
    • Guimaraes KS, Jothi R, Zotenko E, Przytycka TM. Predicting domain-domain interactions using a parsimony approach. Genome Biology 2006, 7:R104. 10.1186/gb-2006-7-11-r104, 1794579, 17094802.
    • (2006) Genome Biology , vol.7
    • Guimaraes, K.S.1    Jothi, R.2    Zotenko, E.3    Przytycka, T.M.4
  • 22
    • 70449707137 scopus 로고    scopus 로고
    • Evaluation of different domain-based methods in protein interaction prediction
    • 10.1016/j.bbrc.2009.09.130, 19800868
    • Ta HX, Holm L. Evaluation of different domain-based methods in protein interaction prediction. Biochemical and Biophysical Research Communications 2009, 390:357-362. 10.1016/j.bbrc.2009.09.130, 19800868.
    • (2009) Biochemical and Biophysical Research Communications , vol.390 , pp. 357-362
    • Ta, H.X.1    Holm, L.2
  • 25
    • 33751353420 scopus 로고    scopus 로고
    • Modeling Interaction Sites in Protein Domains with Interaction Profile Hidden Markov Models
    • 10.1093/bioinformatics/btl486, 17000753
    • Friedrich T, Pils B, Dandekar T, Schultz J, T M. Modeling Interaction Sites in Protein Domains with Interaction Profile Hidden Markov Models. Bioinformatics 2006, 22:2851-2857. 10.1093/bioinformatics/btl486, 17000753.
    • (2006) Bioinformatics , vol.22 , pp. 2851-2857
    • Friedrich, T.1    Pils, B.2    Dandekar, T.3    Schultz, J.4    T, M.5
  • 28
    • 13444257903 scopus 로고    scopus 로고
    • 3DID: interacting protein domains of known three-dimensional structure
    • 539991, 15608228, Database
    • Stein A, Russell R, Aloy P. 3DID: interacting protein domains of known three-dimensional structure. Nucleic Acids Research 2005, (33 Database):D413-D417. 539991, 15608228.
    • (2005) Nucleic Acids Research , Issue.33
    • Stein, A.1    Russell, R.2    Aloy, P.3
  • 30
    • 33947328242 scopus 로고    scopus 로고
    • Choosing negative examples for the prediction of protein-protein interactions
    • 10.1186/1471-2105-7-S1-S2, 1810313, 16723005
    • Ben-Hur A, Stafford Noble W. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics 2006, 7(Suppl 1):S2. 10.1186/1471-2105-7-S1-S2, 1810313, 16723005.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL 1
    • Ben-Hur, A.1    Stafford Noble, W.2
  • 31
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • 10.1073/pnas.092147999, 122873, 11972061
    • Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002, 99(9):5896-5901. 10.1073/pnas.092147999, 122873, 11972061.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.9 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 33
    • 0022594196 scopus 로고
    • An introduction to hidden Markov models
    • Rabiner LR, Juang BH. An introduction to hidden Markov models. IEEE ASSP Magazine 1986, 3:4-16.
    • (1986) IEEE ASSP Magazine , vol.3 , pp. 4-16
    • Rabiner, L.R.1    Juang, B.H.2
  • 36
    • 0037250158 scopus 로고    scopus 로고
    • InterPreTS: protein Interaction Prediction through Tertiary Structure
    • 10.1093/bioinformatics/19.1.161, 12499311
    • Aloy P, Russell RB. InterPreTS: protein Interaction Prediction through Tertiary Structure. Bioinformatics 2003, 19:161-162. 10.1093/bioinformatics/19.1.161, 12499311.
    • (2003) Bioinformatics , vol.19 , pp. 161-162
    • Aloy, P.1    Russell, R.B.2
  • 37
    • 34547581834 scopus 로고    scopus 로고
    • 3D-partner: a web server to infer interacting partners and binding models
    • 10.1093/nar/gkm346, 1933210, 17517763, Web Server
    • Chen YC, Lo YS, Hsu WC, Yang JM. 3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Research 2007, (35 Web Server):W561-W567. 10.1093/nar/gkm346, 1933210, 17517763.
    • (2007) Nucleic Acids Research , Issue.35
    • Chen, Y.C.1    Lo, Y.S.2    Hsu, W.C.3    Yang, J.M.4
  • 38
    • 0035873996 scopus 로고    scopus 로고
    • Fibroblast growth factor homologous factors are intracellular signaling proteins
    • 10.1016/S0960-9822(01)00232-9, 11378392
    • Schoorlemmer J, Goldfarb M. Fibroblast growth factor homologous factors are intracellular signaling proteins. Current Biology 2001, 11:793-797. 10.1016/S0960-9822(01)00232-9, 11378392.
    • (2001) Current Biology , vol.11 , pp. 793-797
    • Schoorlemmer, J.1    Goldfarb, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.