메뉴 건너뛰기




Volumn 20, Issue 7-8, 2009, Pages 741-754

Data-driven model for the prediction of protein transmembrane regions

Author keywords

Amino acid adjacency matrix; Counter propagation artificial neural network; Kohonen map; Protein descriptors; Transmembrane protein; Transmembrane region prediction tool

Indexed keywords

BIOINFORMATICS; FORECASTING; NEURAL NETWORKS;

EID: 72149105294     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/10629360903438602     Document Type: Article
Times cited : (12)

References (38)
  • 2
    • 10244252813 scopus 로고    scopus 로고
    • Transmembrane Proteins in the Protein Data Bank: Identification and Classification
    • Database available at
    • G.E. Tusnady, Z. Dosztanyi, and I. Simon, Transmembrane Proteins in the Protein Data Bank: Identification and Classification, Bioinformatics 20 (2004), pp. 2964-2972, Database available at http://pdbtm.enzim.hu/
    • (2004) Bioinformatics , vol.20 , pp. 2964-2972
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 3
    • 85195049052 scopus 로고    scopus 로고
    • State-of-the-art in membrane protein prediction
    • C.P. Chen and B. Rost, State-of-the-art in membrane protein prediction, Appl. Bioinformatics 1 (2000), pp. 121-135.
    • (2000) Appl. Bioinformatics , vol.1 , pp. 121-135
    • Chen, C.P.1    Rost, B.2
  • 4
    • 0036893269 scopus 로고    scopus 로고
    • Transmembrane helix predictions revisited
    • C.P. Chen, A. Kernytsky, and B. Rost, Transmembrane helix predictions revisited, Protein Sci. 11 (2002), pp. 2774-2791.
    • (2002) Protein Sci. , vol.11 , pp. 2774-2791
    • Chen, C.P.1    Kernytsky, A.2    Rost, B.3
  • 5
    • 34249683488 scopus 로고    scopus 로고
    • Membrane protein structure: Prediction versus reality
    • A. Elofsson and G. von Heijne, Membrane protein structure: Prediction versus reality, Annu. Rev. Biochem. 76 (2007), pp. 125-140.
    • (2007) Annu. Rev. Biochem. , vol.76 , pp. 125-140
    • Elofsson, A.1    von Heijne, G.2
  • 6
    • 85195030324 scopus 로고    scopus 로고
    • Perl 5.10.1, Software available at
    • Perl 5.10.1 The Perl Foundation, 2007; Software available at http://www.perl.org/
    • (2007) The Perl Foundation
  • 8
    • 47349096545 scopus 로고    scopus 로고
    • Representation of proteins as walks in 20-D space
    • M. Novič and M. Randić, Representation of proteins as walks in 20-D space, SAR QSAR Environ. Res. 19(3) (2008), pp. 317-337.
    • (2008) Sar Qsar Environ. Res. , vol.19 , Issue.3 , pp. 317-337
    • Novič, M.1    Randić, M.2
  • 9
    • 47349126419 scopus 로고    scopus 로고
    • On novel representation of proteins based on amino acid adjacency matrix
    • M. Randić, M. Novič, and M. Vračko, On novel representation of proteins based on amino acid adjacency matrix, SAR QSAR Environ. Res. 19 (2008), pp. 339-349.
    • (2008) Sar Qsar Environ. Res. , vol.19 , pp. 339-349
    • Randić, M.1    Novič, M.2    Vračko, M.3
  • 10
    • 0019883174 scopus 로고
    • Affinities of amino acid side chains for solvent water
    • R. Wolfenden, L. Andersson, P. Cullis, and C. Southgate, Affinities of amino acid side chains for solvent water, Biochemistry 20 (1981), pp. 849-855.
    • (1981) Biochemistry , vol.20 , pp. 849-855
    • Wolfenden, R.1    Andersson, L.2    Cullis, P.3    Southgate, C.4
  • 11
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • J. Kyte and R. Doolite, A simple method for displaying the hydropathic character of a protein, J. Mol Biol. 157 (1982), pp. 105-132.
    • (1982) J. Mol Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolite, R.2
  • 12
    • 0020371598 scopus 로고
    • The structural dependence of amino acid hydrophobicity parameters
    • M. Charton and B.I. Charton, The structural dependence of amino acid hydrophobicity parameters, J. Theor. Biol. 99 (1982), pp. 629-644.
    • (1982) J. Theor. Biol. , vol.99 , pp. 629-644
    • Charton, M.1    Charton, B.I.2
  • 13
    • 0022412192 scopus 로고
    • Hydrophobicity of amino acid residues in globular proteins
    • G. Rose, A. Geselowitz, G. Lesser, R. Lee, and M. Zehfus, Hydrophobicity of amino acid residues in globular proteins, Science 229 (1985), pp. 834-838.
    • (1985) Science , vol.229 , pp. 834-838
    • Rose, G.1    Geselowitz, A.2    Lesser, G.3    Lee, R.4    Zehfus, M.5
  • 14
    • 0023515080 scopus 로고
    • Counterpropagation networks
    • R. Hecht-Nielsen, Counterpropagation networks, Appl. Opt. 26 (1987), pp. 4979-4984.
    • (1987) Appl. Opt. , vol.26 , pp. 4979-4984
    • Hecht-Nielsen, R.1
  • 15
    • 0030737774 scopus 로고    scopus 로고
    • Kohonen and counterpropagation artificial neural networks in analytical chemistry
    • J. Zupan, M. Novič, and I. Ruisanchez, Kohonen and counterpropagation artificial neural networks in analytical chemistry, Chemom. Int. Lab. Syst. 38 (1997), pp. 1-23.
    • (1997) Chemom. Int. Lab. Syst. , vol.38 , pp. 1-23
    • Zupan, J.1    Novič, M.2    Ruisanchez, I.3
  • 17
    • 0343017182 scopus 로고
    • Investigation of infrared spectra-structure correlation using Kohonen and counterpropagation neural network
    • M. Novič and J. Zupan, Investigation of infrared spectra-structure correlation using Kohonen and counterpropagation neural network, J. Chem. Inf. Comput. Sci. 35 (1995), pp. 454-466.
    • (1995) J. Chem. Inf. Comput. Sci. , vol.35 , pp. 454-466
    • Novič, M.1    Zupan, J.2
  • 18
    • 0038724207 scopus 로고    scopus 로고
    • The importance of being earnest: Validation is absolute essential for successful application and interpretation of QSPR models
    • A. Tropsha, P. Gramatica, and V.K. Gombar, The importance of being earnest: Validation is absolute essential for successful application and interpretation of QSPR models, QSAR Comb. Sci. 22 (2003), pp. 69-77.
    • (2003) Qsar Comb. Sci. , vol.22 , pp. 69-77
    • Tropsha, A.1    Gramatica, P.2    Gombar, V.K.3
  • 21
    • 0032577917 scopus 로고    scopus 로고
    • The bilirubin-binding motif of bilitranslocase and its relation to conserved motifs in ancient biliproteins
    • L. Battiston, S. Passamonti, A. Macango, and G.L. Sottocasa, The bilirubin-binding motif of bilitranslocase and its relation to conserved motifs in ancient biliproteins, Biochem. Biophys. Res. Commun. 247(3) (1998), pp. 687-692.
    • (1998) Biochem. Biophys. Res. Commun. , vol.247 , Issue.3 , pp. 687-692
    • Battiston, L.1    Passamonti, S.2    Macango, A.3    Sottocasa, G.L.4
  • 22
    • 68349144331 scopus 로고    scopus 로고
    • Bioavailability of flavonoids: A review of their membrane transport and the function of bilitranslocase in animal and plant organisms
    • S. Passamonti, M. Terdoslavich, R. Franca, A. Vanzo, F. Tramer, E. Braidot, E. Petrussa, and A. Vianello, Bioavailability of flavonoids: A review of their membrane transport and the function of bilitranslocase in animal and plant organisms, Curr. Drug Metab. 10 (2009), pp. 369-394.
    • (2009) Curr. Drug Metab , vol.10 , pp. 369-394
    • Passamonti, S.1    Terdoslavich, M.2    Franca, R.3    Vanzo, A.4    Tramer, F.5    Braidot, E.6    Petrussa, E.7    Vianello, A.8
  • 24
    • 22144495427 scopus 로고    scopus 로고
    • A characterization of electrogenic bromosulfopthalein transport in carnation petal microsomes and its inhibition by antibodies against bilitranslocase
    • S. Passamonti, A. Cocolo, E. Braidot, E. Petrussa, C. Peresson, N. Medic, F. Macri, and A. Vianello, A characterization of electrogenic bromosulfopthalein transport in carnation petal microsomes and its inhibition by antibodies against bilitranslocase, FEBS J. 272 (2005), pp. 3282-3296.
    • (2005) Febs J , vol.272 , pp. 3282-3296
    • Passamonti, S.1    Cocolo, A.2    Braidot, E.3    Petrussa, E.4    Peresson, C.5    Medic, N.6    Macri, F.7    Vianello, A.8
  • 25
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Available at
    • D.T. Jones, W.R. Taylor, and J.M. Thornton, A model recognition approach to the prediction of all-helical membrane protein structure and topology, Biochemistry 33 (1994), pp. 3038-3049. Available at http://saier-144-37.ucsd.edu/memsat.html
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 26
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: Applications to topology prediction
    • Available at
    • G.E. Tusnády and I. Simon, Principles governing amino acid composition of integral membrane proteins: Applications to topology prediction, J. Mol. Biol. 283 (1998), pp. 489-506. Available at http://www.enzim.hu/hmmtop/html/adv_submit.html
    • (1998) J. Mol. Biol. , vol.283 , pp. 489-506
    • Tusnády, G.E.1    Simon, I.2
  • 27
    • 3242885293 scopus 로고    scopus 로고
    • The predict protein server
    • Available at
    • B. Rost, G. Yachdav, and J. Liu, The predict protein server, Nucl. Acids Res. 32 (2004), pp. W321-W326. Available at http://www.predictprotein.org/main.php
    • (2004) Nucl. Acids Res. , vol.32
    • Rost, B.1    Yachdav, G.2    Liu, J.3
  • 28
    • 0000207681 scopus 로고
    • Tmbase - A database of membrane spanning proteins segments
    • Hoppe-Seyler, Available at
    • K. Hofmann and W. Stoffel, Tmbase - A database of membrane spanning proteins segments, Biol. Chem. Hoppe-Seyler 374 (1993), pp. 166. Available at http://www.ch.embnet.org/software/ TMPRED_form.html
    • (1993) Biol. Chem , vol.374 , pp. 166
    • Hofmann, K.1    Stoffel, W.2
  • 29
    • 0028568176 scopus 로고
    • TopPred II: An improved software for membrane protein structure predictions
    • Available at
    • M.G. Claros and G. von Heijne, TopPred II: An improved software for membrane protein structure predictions, CABIOS 10 (1994), pp. 685-686. Available at http://mobyle.pasteur.fr/cgi- bin/portal.py?form1=/4toppred
    • (1994) Cabios , vol.10 , pp. 685-686
    • Claros, M.G.1    von Heijne, G.2
  • 30
    • 1842789432 scopus 로고    scopus 로고
    • SVMtm: Support vector machines to predict transmembrane segments
    • Available at
    • Z. Yuan, J.S. Mattick, and R.D. Teasdale, SVMtm: Support vector machines to predict transmembrane segments, J. Comput. Chem. 25(5) (2004), pp. 632-636. Available at http:// ccb.imb.uq.edu.au/svmtm/
    • (2004) J. Comput. Chem , vol.25 , Issue.5 , pp. 632-636
    • Yuan, Z.1    Mattick, J.S.2    Teasdale, R.D.3
  • 31
    • 8444222703 scopus 로고    scopus 로고
    • WaveTM: Wavelet-based transmembrane segment prediction
    • Available at
    • E.E. Pashou, Z.I. Litou, Th.D. Liakopoulos, and S.J. Hamodrakas, waveTM: Wavelet-based transmembrane segment prediction, In Silico Biol. 4 (2004), pp. 0012. Available at http:// athina.biol.uoa.gr/bioinformatics/waveTM/
    • (2004) Silico Biol , vol.4 , pp. 0012
    • Pashou, E.E.1    Litou, Z.I.2    Liakopoulos, T.D.3    Hamodrakas, S.J.4
  • 32
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • Available at
    • L. Kall, A. Krogh, and E. Sonnhammer, A combined transmembrane topology and signal peptide prediction method, J. Mol. Biol. 338 (2004), pp. 1027-1036. Available at http://phobius.sbc.su.se/
    • (2004) J. Mol. Biol. , vol.338 , pp. 1027-1036
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.3
  • 33
    • 57149112523 scopus 로고    scopus 로고
    • Transmembrane topology and signal prediction using Dynamic Bayesian Networks
    • e1000213, Available at
    • S.M. Reynolds, L. Kall, M.E. Riffle, J.A. Bilmes, and W.S. Noble, Transmembrane topology and signal prediction using Dynamic Bayesian Networks, PLoS Comput. Biol. 4 (2008), e1000213. Available at http://www.yeastrc.org/philius/pages/philius/runPhilius.jsp
    • (2008) Plos Comput. Biol , vol.4
    • Reynolds, S.M.1    Kall, L.2    Riffle, M.E.3    Bilmes, J.A.4    Noble, W.S.5
  • 35
    • 3242891271 scopus 로고    scopus 로고
    • ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability
    • Available at
    • M. Arai, H. Mitsuke, M. Ikeda, J.X. Xia, T. Kikuchi, M. Satake, and T. Shimizu, ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability, Nucl. Acids Res. 32 (2004), pp. W390-W393. Available at http://bioinfo.si.hirosaki-u.ac.jp/ ConPred2/
    • (2004) Nucl. Acids Res. , vol.32
    • Arai, M.1    Mitsuke, H.2    Ikeda, M.3    Xia, J.X.4    Kikuchi, T.5    Satake, M.6    Shimizu, T.7
  • 36
    • 53849100320 scopus 로고    scopus 로고
    • IgTm: An algorithm to predict transmembrane domains and topology in proteins
    • Available at
    • P. Piedachu, D. Lopez, and M. Campos, IgTm: An algorithm to predict transmembrane domains and topology in proteins, BMC Bioinfo. 9 (2008), pp. 367-377. Available at www.dsic.upv.es/ users/tlcc/bio/bio.html
    • (2008) Bmc Bioinfo. , vol.9 , pp. 367-377
    • Piedachu, P.1    Lopez, D.2    Campos, M.3
  • 37
    • 33847155026 scopus 로고    scopus 로고
    • Algorithms for incorporating prior topological information in HMMs: Application to transmembrane proteins
    • Available at
    • P.G. Bagos, T.D. Liakopoulos, and S.J. Hamodrakas, Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins, BMC Bioinfo. 7 (2006), pp. 189-205. Available at http://bioinformatics.biol.uoa.gr/HMM-TM/input.jsp
    • (2006) Bmc Bioinfo. , vol.7 , pp. 189-205
    • Bagos, P.G.1    Liakopoulos, T.D.2    Hamodrakas, S.J.3
  • 38
    • 85195102927 scopus 로고    scopus 로고
    • Tmpro: Transmembrane helix prediction through amino acid property analysis
    • Available at
    • M. Ganapathiraju, C.J. Jursa, H.A. Karimi, and J. Klein-Seetharaman, Tmpro: Transmembrane helix prediction through amino acid property analysis, Bioinfo. Adv. Acc. (2007). Available at http://linzer.blm.cs.cmu.edu/tmpro/
    • (2007) Bioinfo. Adv. Acc.
    • Ganapathiraju, M.1    Jursa, C.J.2    Karimi, H.A.3    Klein-Seetharaman, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.