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Volumn 11, Issue 7, 2010, Pages 550-561

Topology prediction of Helical Transmembrane proteins: How far have we reached?

Author keywords

Hidden Markov model; Machine learning algorithm; Support vector machine; Topology prediction; Transmembrane protein

Indexed keywords

GLOBULAR PROTEIN; MEMBRANE PROTEIN; SIGNAL PEPTIDE;

EID: 79251519929     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920310794109184     Document Type: Article
Times cited : (32)

References (128)
  • 1
    • 0037020329 scopus 로고    scopus 로고
    • Drug design strategies for targeting Gprotein-coupled receptors
    • Klabunde, T.; Hessler, G. Drug design strategies for targeting Gprotein-coupled receptors. Chembiochem, 2002, 3(10), 928-944.
    • (2002) Chembiochem , vol.3 , Issue.10 , pp. 928-944
    • Klabunde, T.1    Hessler, G.2
  • 2
    • 33845275819 scopus 로고    scopus 로고
    • Estimation of membrane proteins in the human proteome
    • Ahram, M.; Litou, Z.I.; Fang, R.; Al-Tawallbeh, G. Estimation of membrane proteins in the human proteome. In Silico Biol., 2006, 6(5), 379-386.
    • (2006) In Silico Biol , vol.6 , Issue.5 , pp. 379-386
    • Ahram, M.1    Litou, Z.I.2    Fang, R.3    Al-Tawallbeh, G.4
  • 3
    • 0032570779 scopus 로고    scopus 로고
    • Do transmembrane protein superfolds exist?
    • Jones, D.T. Do transmembrane protein superfolds exist? FEBS Lett., 1998, 423(3), 281-285.
    • (1998) FEBS Lett , vol.423 , Issue.3 , pp. 281-285
    • Jones, D.T.1
  • 4
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 2001, 305(3), 567-580.
    • (2001) J. Mol. Biol , vol.305 , Issue.3 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 5
    • 0033552649 scopus 로고    scopus 로고
    • Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system
    • Mitaku, S.; Ono, M.; Hirokawa, T.; Boon-Chieng, S.; Sonoyama, M. Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system. Biophys. Chem., 1999, 82(2-3), 165-171.
    • (1999) Biophys. Chem. , vol.82 , Issue.2-3 , pp. 165-171
    • Mitaku, S.1    Ono, M.2    Hirokawa, T.3    Boon-Chieng, S.4    Sonoyama, M.5
  • 6
    • 10244252813 scopus 로고    scopus 로고
    • Transmembrane proteins in the Protein Data Bank: Identification and classification
    • Tusnády, G.; Dosztányi, Z.; Simon, I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics, 2004, 20(17), 2964-2972.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 2964-2972
    • Tusnády, G.1    Dosztányi, Z.2    Simon, I.3
  • 7
    • 13444280419 scopus 로고    scopus 로고
    • PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank
    • Tusnády, G.; Dosztányi, Z.; Simon, I. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res., 2005, 33(Database issue), D275-D278.
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database issue
    • Tusnády, G.1    Dosztányi, Z.2    Simon, I.3
  • 9
    • 0030983047 scopus 로고    scopus 로고
    • Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria
    • Wallin, E.; Tsukihara, T.; Yoshikawa, S.; von Heijne, G.; Elofsson, A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci., 1997, 6(4), 808-815.
    • (1997) Protein Sci , vol.6 , Issue.4 , pp. 808-815
    • Wallin, E.1    Tsukihara, T.2    Yoshikawa, S.3    von Heijne, G.4    Elofsson, A.5
  • 10
    • 12344330612 scopus 로고    scopus 로고
    • A study of the membrane-water interface region of membrane proteins
    • Granseth, E.; von Heijne, G.; Elofsson, A. A study of the membrane-water interface region of membrane proteins. J. Mol. Biol., 2005, 346(1), 377-385.
    • (2005) J. Mol. Biol , vol.346 , Issue.1 , pp. 377-385
    • Granseth, E.1    von Heijne, G.2    Elofsson, A.3
  • 11
    • 34548178234 scopus 로고    scopus 로고
    • Antidepressant binding site in a bacterial homologue of neurotransmitter transporters
    • Singh, S.K.; Yamashita, A.; Gouaux, E. Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature, 2007, 448(7156), 952-956.
    • (2007) Nature , vol.448 , Issue.7156 , pp. 952-956
    • Singh, S.K.1    Yamashita, A.2    Gouaux, E.3
  • 12
    • 33746361201 scopus 로고    scopus 로고
    • Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: Application to complete genomes
    • Viklund, H.; Granseth, E.; Elofsson, A. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J. Mol. Biol., 2006, 361(3), 591-603.
    • (2006) J. Mol. Biol , vol.361 , Issue.3 , pp. 591-603
    • Viklund, H.1    Granseth, E.2    Elofsson, A.3
  • 13
    • 0025782832 scopus 로고
    • Proline kinks in transmembrane alpha-helices
    • von Heijne, G. Proline kinks in transmembrane alpha-helices. J. Mol. Biol., 1991, 218(3), 499-503.
    • (1991) J. Mol. Biol , vol.218 , Issue.3 , pp. 499-503
    • von Heijne, G.1
  • 14
    • 0031047328 scopus 로고    scopus 로고
    • Roles of transmembrane prolines and proline-induced kinks of the lutropin/choriogonadotropin receptor
    • Hong, S.; Ryu, K.S.; Oh, M.S.; Ji, I.; Ji, T.H. Roles of transmembrane prolines and proline-induced kinks of the lutropin/choriogonadotropin receptor. J. Biol. Chem., 1997, 272(7), 4166-4171.
    • (1997) J. Biol. Chem , vol.272 , Issue.7 , pp. 4166-4171
    • Hong, S.1    Ryu, K.S.2    Oh, M.S.3    Ji, I.4    Ji, T.H.5
  • 15
    • 0035895421 scopus 로고    scopus 로고
    • Non-alphahelical elements modulate polytopic membrane protein architecture
    • Riek, R.P.; Rigoutsos, I.; Novotny, J.; Graham, R.M. Non-alphahelical elements modulate polytopic membrane protein architecture. J. Mol. Biol., 2001, 306(2), 349-362.
    • (2001) J. Mol. Biol , vol.306 , Issue.2 , pp. 349-362
    • Riek, R.P.1    Rigoutsos, I.2    Novotny, J.3    Graham, R.M.4
  • 16
    • 0742288411 scopus 로고    scopus 로고
    • The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
    • Yohannan, S.; Faham, S.; Yang, D.; Whitelegge, J.P.; Bowie, J.U. The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc. Natl. Acad. Sci. USA, 2004, 101(4), 959-963.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.4 , pp. 959-963
    • Yohannan, S.1    Faham, S.2    Yang, D.3    Whitelegge, J.P.4    Bowie, J.U.5
  • 17
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • Chothia, C. Proteins. One thousand families for the molecular biologist. Nature, 1992, 357(6379), 543-544.
    • (1992) Nature , vol.357 , Issue.6379 , pp. 543-544
    • Chothia, C.1
  • 18
    • 0034674175 scopus 로고    scopus 로고
    • Estimating the number of protein folds and families from complete genome data
    • Wolf, Y.I.; Grishin, N.V.; Koonin, E.V. 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
  • 19
    • 0037079014 scopus 로고    scopus 로고
    • The structure of the protein universe and genome evolution
    • Koonin, E.V.; Wolf, Y.I.; Karev, G.P. The structure of the protein universe and genome evolution. Nature, 2002, 420(6912), 218-223.
    • (2002) Nature , vol.420 , Issue.6912 , pp. 218-223
    • Koonin, E.V.1    Wolf, Y.I.2    Karev, G.P.3
  • 20
    • 0033457943 scopus 로고    scopus 로고
    • Helix-bundle membrane protein fold templates
    • Bowie, J.U. Helix-bundle membrane protein fold templates. Protein Sci., 1999, 8(12), 2711-2719.
    • (1999) Protein Sci , vol.8 , Issue.12 , pp. 2711-2719
    • Bowie, J.U.1
  • 21
    • 0034057802 scopus 로고    scopus 로고
    • Membrane topology and insertion of membrane proteins: Search for topogenic signals
    • van Geest, M.; Lolkema, J.S. Membrane topology and insertion of membrane proteins: search for topogenic signals. Microbiol. Mol. Biol. Rev., 2000, 64(1), 13-33.
    • (2000) Microbiol. Mol. Biol. Rev , vol.64 , Issue.1 , pp. 13-33
    • van Geest, M.1    Lolkema, J.S.2
  • 22
    • 38549172064 scopus 로고    scopus 로고
    • TOPDB: Topology data bank of transmembrane proteins
    • Tusnády, G.E.; Kalmár, L.; Simon, I. TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res., 2008, 36(Database issue), D234-D239.
    • (2008) Nucleic Acids Res , vol.36 , Issue.Database issue
    • Tusnády, G.E.1    Kalmár, L.2    Simon, I.3
  • 23
    • 19744376674 scopus 로고    scopus 로고
    • Global topology analysis of the Escherichia coli inner membrane proteome
    • Daley, D.O.; Rapp, M.; Granseth, E.; Melén, K.; Drew, D.; von Heijne, G. Global topology analysis of the Escherichia coli inner membrane proteome. Science, 2005, 308(5726), 1321-1323.
    • (2005) Science , vol.308 , Issue.5726 , pp. 1321-1323
    • Daley, D.O.1    Rapp, M.2    Granseth, E.3    Melén, K.4    Drew, D.5    von Heijne, G.6
  • 24
    • 33746616385 scopus 로고    scopus 로고
    • A global topology map of the Saccharomyces cerevisiae membrane proteome
    • Kim, H.; Melén, K.; Osterberg, M.; von Heijne, G. A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc. Natl. Acad. Sci. USA, 2006, 103(30), 11142-11147.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , Issue.30 , pp. 11142-11147
    • Kim, H.1    Melén, K.2    Osterberg, M.3    von Heijne, G.4
  • 25
    • 0000651660 scopus 로고
    • The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology
    • von Heijne, G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology. EMBO J., 1986, 5(11), 3021-3027.
    • (1986) EMBO J , vol.5 , Issue.11 , pp. 3021-3027
    • von Heijne, G.1
  • 26
    • 0025015646 scopus 로고
    • Fine-tuning the topology of a polytopic membrane protein: Role of positively and negatively charged amino acids
    • Nilsson, I.; von Heijne, G. Fine-tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids. Cell, 1990, 62(6), 1135-1141.
    • (1990) Cell , vol.62 , Issue.6 , pp. 1135-1141
    • Nilsson, I.1    von Heijne, G.2
  • 27
    • 0028175016 scopus 로고
    • Topological frustration in multispanning E. coli inner membrane proteins
    • Gafvelin, G.; von Heijne, G. Topological frustration in multispanning E. coli inner membrane proteins. Cell, 1994, 77(3), 401-412.
    • (1994) Cell , vol.77 , Issue.3 , pp. 401-412
    • Gafvelin, G.1    von Heijne, G.2
  • 28
    • 32244436490 scopus 로고    scopus 로고
    • Identification and evolution of dual-topology membrane proteins
    • Rapp, M.; Granseth, E.; Seppälä, S.; von Heijne, G. Identification and evolution of dual-topology membrane proteins. Nat. Struct. Mol. Biol., 2006, 13(2), 112-116.
    • (2006) Nat. Struct. Mol. Biol , vol.13 , Issue.2 , pp. 112-116
    • Rapp, M.1    Granseth, E.2    Seppälä, S.3    von Heijne, G.4
  • 29
    • 29344450131 scopus 로고    scopus 로고
    • X-ray structure of the EmrE multidrug transporter in complex with a substrate
    • Pornillos, O.; Chen, Y.; Chen, A.P.; Chang, G. X-ray structure of the EmrE multidrug transporter in complex with a substrate. Science, 2005, 310(5756), 1950-1953.
    • (2005) Science , vol.310 , Issue.5756 , pp. 1950-1953
    • Pornillos, O.1    Chen, Y.2    Chen, A.P.3    Chang, G.4
  • 32
    • 34249899930 scopus 로고    scopus 로고
    • When biochemistry meets structural biology: The cautionary tale of EmrE
    • Schuldiner, S. When biochemistry meets structural biology: the cautionary tale of EmrE. Trends Biochem Sci, 2007, 32(6), 252-258.
    • (2007) Trends Biochem Sci , vol.32 , Issue.6 , pp. 252-258
    • Schuldiner, S.1
  • 33
    • 34547863829 scopus 로고    scopus 로고
    • Controversy over EmrE structure
    • author reply 748-751
    • Schuldiner, S. Controversy over EmrE structure. Science, 2007, 317(5839), 748-51 author reply 748-751.
    • (2007) Science , vol.317 , Issue.5839 , pp. 748-751
    • Schuldiner, S.1
  • 36
    • 0036893269 scopus 로고    scopus 로고
    • Transmembrane helix predictions revisited
    • Chen, C.P.; Kernytsky, A.; Rost, B. Transmembrane helix predictions revisited. Protein Sci., 2002, 11(12), 2774-2791.
    • (2002) Protein Sci , vol.11 , Issue.12 , pp. 2774-2791
    • Chen, C.P.1    Kernytsky, A.2    Rost, B.3
  • 37
    • 34249683488 scopus 로고    scopus 로고
    • Membrane protein structure: Prediction versus reality
    • Elofsson, A.; von Heijne, G. Membrane protein structure: prediction versus reality. Annu. Rev. Biochem., 2007, 76, 125-140.
    • (2007) Annu. Rev. Biochem , vol.76 , pp. 125-140
    • Elofsson, A.1    von Heijne, G.2
  • 39
    • 0001911218 scopus 로고    scopus 로고
    • State-of-the-art in membrane protein prediction
    • Chen, C.P.; Rost, B. State-of-the-art in membrane protein prediction. Appl. Bioinformatics, 2002, 1(1), 21-35.
    • (2002) Appl. Bioinformatics , vol.1 , Issue.1 , pp. 21-35
    • Chen, C.P.1    Rost, B.2
  • 41
    • 0030759333 scopus 로고    scopus 로고
    • Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method
    • Cserz, M.; Wallin, E.; Simon, I.; von Heijne, G.; Elofsson, A. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng., 1997, 10(6), 673-676.
    • (1997) Protein Eng , vol.10 , Issue.6 , pp. 673-676
    • Cserz, M.1    Wallin, E.2    Simon, I.3    von Heijne, G.4    Elofsson, A.5
  • 42
    • 0036763207 scopus 로고    scopus 로고
    • On filtering false positive transmembrane protein predictions
    • Cserz, M.; Eisenhaber, F.; Eisenhaber, B.; Simon, I. On filtering false positive transmembrane protein predictions. Protein Eng., 2002, 15(9), 745-752.
    • (2002) Protein Eng , vol.15 , Issue.9 , pp. 745-752
    • Cserz, M.1    Eisenhaber, F.2    Eisenhaber, B.3    Simon, I.4
  • 43
    • 0347093547 scopus 로고    scopus 로고
    • TM or not TM: Transmembrane protein prediction with low false positive rate using DAS-TMfilter
    • Cserz, M.; Eisenhaber, F.; Eisenhaber, B.; Simon, I. TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics, 2004, 20(1), 136-137.
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 136-137
    • Cserz, M.1    Eisenhaber, F.2    Eisenhaber, B.3    Simon, I.4
  • 44
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
    • Tusnády, G.E.; Simon, I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol., 1998, 283(2), 489-506.
    • (1998) J. Mol. Biol , vol.283 , Issue.2 , pp. 489-506
    • Tusnády, G.E.1    Simon, I.2
  • 45
    • 3042579686 scopus 로고    scopus 로고
    • Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
    • Viklund, H.; Elofsson, A. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci., 2004, 13(7), 1908-1917.
    • (2004) Protein Sci , vol.13 , Issue.7 , pp. 1908-1917
    • Viklund, H.1    Elofsson, A.2
  • 46
    • 18744403991 scopus 로고    scopus 로고
    • An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
    • Kahsay, R.Y.; Gao, G.; Liao, L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics, 2005, 21(9), 1853-1858.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1853-1858
    • Kahsay, R.Y.1    Gao, G.2    Liao, L.3
  • 47
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • Käll, L.; Krogh, A.; Sonnhammer, E.L.L. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 2004, 338(5), 1027-1036.
    • (2004) J. Mol. Biol , vol.338 , Issue.5 , pp. 1027-1036
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 48
    • 29144483361 scopus 로고    scopus 로고
    • An HMM posterior decoder for sequence feature prediction that includes homology information
    • Käll, L.; Krogh, A.; Sonnhammer, E.L.L. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics, 2005, 21(Suppl 1), i251-i257.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 49
    • 34547584314 scopus 로고    scopus 로고
    • Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
    • Käll, L.; Krogh, A.; Sonnhammer, E.L.L. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res., 2007, 35(Web Server issue), W429-W432.
    • (2007) Nucleic Acids Res , vol.35 , Issue.Web Server issue
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 50
    • 57149112523 scopus 로고    scopus 로고
    • Transmembrane topology and signal peptide prediction using dynamic bayesian networks
    • Reynolds, S.M.; Käll, L.; Riffle, M.E.; Bilmes, J.A.; Noble, W.S. Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput. Biol., 2008, 4(11), e1000213.
    • (2008) PLoS Comput. Biol , vol.4 , Issue.11
    • Reynolds, S.M.1    Käll, L.2    Riffle, M.E.3    Bilmes, J.A.4    Noble, W.S.5
  • 51
    • 34250883824 scopus 로고    scopus 로고
    • Transmembrane helix and topology prediction using hierarchical SVM classifiers and an alternating geometric scoring function
    • Lo, A.; Chiu, H.; Sung, T.; Hsu, W. Transmembrane helix and topology prediction using hierarchical SVM classifiers and an alternating geometric scoring function. Comput. Syst. Bioinformatics Conf., 2006, 31-42.
    • (2006) Comput. Syst. Bioinformatics Conf , pp. 31-42
    • Lo, A.1    Chiu, H.2    Sung, T.3    Hsu, W.4
  • 52
    • 39749179168 scopus 로고    scopus 로고
    • Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function
    • Lo, A.; Chiu, H.; Sung, T.; Lyu, P.; Hsu, W. Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J. Proteome Res., 2008, 7(2), 487-496.
    • (2008) J. Proteome Res , vol.7 , Issue.2 , pp. 487-496
    • Lo, A.1    Chiu, H.2    Sung, T.3    Lyu, P.4    Hsu, W.5
  • 53
    • 35748979116 scopus 로고    scopus 로고
    • TMpro web server and web service: Transmembrane helix prediction through amino acid property analysis
    • Ganapathiraju, M.; Jursa, C.J.; Karimi, H.A.; Klein-Seetharaman, J. TMpro web server and web service: transmembrane helix prediction through amino acid property analysis. Bioinformatics, 2007, 23(20), 2795-2796.
    • (2007) Bioinformatics , vol.23 , Issue.20 , pp. 2795-2796
    • Ganapathiraju, M.1    Jursa, C.J.2    Karimi, H.A.3    Klein-Seetharaman, J.4
  • 54
    • 84872004750 scopus 로고    scopus 로고
    • Transmembrane helix prediction using amino acid property features and latent semantic analysis
    • Ganapathiraju, M.; Balakrishnan, N.; Reddy, R.; Klein-Seetharaman, J. Transmembrane helix prediction using amino acid property features and latent semantic analysis. BMC Bioinformatics, 2008, 9(Suppl 1), S4.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 1
    • Ganapathiraju, M.1    Balakrishnan, N.2    Reddy, R.3    Klein-Seetharaman, J.4
  • 56
    • 26444578263 scopus 로고    scopus 로고
    • SOSUIsignal: Software system for prediction of signal peptide and membrane protein
    • Gomi, M.; Akazawa, F.; Mitaku, S. SOSUIsignal: software system for prediction of signal peptide and membrane protein. Genome Informatics, 2000, 11, 414-415.
    • (2000) Genome Informatics , vol.11 , pp. 414-415
    • Gomi, M.1    Akazawa, F.2    Mitaku, S.3
  • 57
    • 0344064078 scopus 로고    scopus 로고
    • Computational differentiation of N-terminal signal peptides and transmembrane helices
    • Yuan, Z.; Davis, M.J.; Zhang, F.; Teasdale, R.D. Computational differentiation of N-terminal signal peptides and transmembrane helices. Biochem. Biophys. Res. Commun., 2003, 312(4), 1278-1283.
    • (2003) Biochem. Biophys. Res. Commun , vol.312 , Issue.4 , pp. 1278-1283
    • Yuan, Z.1    Davis, M.J.2    Zhang, F.3    Teasdale, R.D.4
  • 58
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen, H.; Engelbrecht, J.; Brunak, S.; von Heijne, G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 1997, 10(1), 1-6.
    • (1997) Protein Eng , vol.10 , Issue.1 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    von Heijne, G.4
  • 59
    • 0033044637 scopus 로고    scopus 로고
    • Machine learning approaches for the prediction of signal peptides and other protein sorting signals
    • Nielsen, H.; Brunak, S.; von Heijne, G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng., 1999, 12(1), 3-9.
    • (1999) Protein Eng , vol.12 , Issue.1 , pp. 3-9
    • Nielsen, H.1    Brunak, S.2    von Heijne, G.3
  • 60
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • Bendtsen, J.D.; Nielsen, H.; von Heijne, G.; Brunak, S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 2004, 340(4), 783-795.
    • (2004) J. Mol. Biol , vol.340 , Issue.4 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    von Heijne, G.3    Brunak, S.4
  • 61
    • 57249083976 scopus 로고    scopus 로고
    • SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology
    • Viklund, H.; Bernsel, A.; Skwark, M.; Elofsson, A. SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology. Bioinformatics, 2008, 24(24), 2928-2929.
    • (2008) Bioinformatics , vol.24 , Issue.24 , pp. 2928-2929
    • Viklund, H.1    Bernsel, A.2    Skwark, M.3    Elofsson, A.4
  • 62
    • 0036936886 scopus 로고    scopus 로고
    • Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction
    • Lao, D.M.; Okuno, T.; Shimizu, T. Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction. In Silico Biol., 2002, 2(4), 485-494.
    • (2002) In Silico Biol , vol.2 , Issue.4 , pp. 485-494
    • Lao, D.M.1    Okuno, T.2    Shimizu, T.3
  • 63
    • 0036947980 scopus 로고    scopus 로고
    • The presence of signal peptide significantly affects transmembrane topology prediction
    • Lao, D.M.; Arai, M.; Ikeda, M.; Shimizu, T. The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics, 2002, 18(12), 1562-1566.
    • (2002) Bioinformatics , vol.18 , Issue.12 , pp. 1562-1566
    • Lao, D.M.1    Arai, M.2    Ikeda, M.3    Shimizu, T.4
  • 64
    • 0023645034 scopus 로고
    • Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins
    • Cornette, J.L.; Cease, K.B.; Margalit, H.; Spouge, J.L.; Berzofsky, J.A.; DeLisi, C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol., 1987, 195(3), 659-685.
    • (1987) J. Mol. Biol , vol.195 , Issue.3 , pp. 659-685
    • Cornette, J.L.1    Cease, K.B.2    Margalit, H.3    Spouge, J.L.4    Berzofsky, J.A.5    Delisi, C.6
  • 66
    • 34247595392 scopus 로고    scopus 로고
    • Experimental measures of amino acid hydrophobicity and the topology of transmembrane and globular proteins
    • Wolfenden, R. Experimental measures of amino acid hydrophobicity and the topology of transmembrane and globular proteins. J. Gen. Physiol., 2007, 129(5), 357-362.
    • (2007) J. Gen. Physiol , vol.129 , Issue.5 , pp. 357-362
    • Wolfenden, R.1
  • 67
    • 0028104942 scopus 로고
    • New alignment strategy for transmembrane proteins
    • Cserz, M.; Bernassau, J.M.; Simon, I.; Maigret, B. New alignment strategy for transmembrane proteins. J. Mol. Biol., 1994, 243(3), 388-396.
    • (1994) J. Mol. Biol , vol.243 , Issue.3 , pp. 388-396
    • Cserz, M.1    Bernassau, J.M.2    Simon, I.3    Maigret, B.4
  • 68
    • 48349146731 scopus 로고    scopus 로고
    • Transmembrane helix prediction in proteins using hydrophobicity properties and higher-order statistics
    • Kitsas, I.K.; Hadjileontiadis, L.J.; Panas, S.M. Transmembrane helix prediction in proteins using hydrophobicity properties and higher-order statistics. Comput. Biol. Med., 2008, 38(8), 867-880.
    • (2008) Comput. Biol. Med , vol.38 , Issue.8 , pp. 867-880
    • Kitsas, I.K.1    Hadjileontiadis, L.J.2    Panas, S.M.3
  • 69
    • 48749084114 scopus 로고    scopus 로고
    • MemBrain: Improving the accuracy of predicting transmembrane helices
    • Shen, H.; Chou, J.J. MemBrain: improving the accuracy of predicting transmembrane helices. PLoS One, 2008, 3(6), e2399.
    • (2008) PLoS One , vol.3 , Issue.6
    • Shen, H.1    Chou, J.J.2
  • 71
    • 2542452829 scopus 로고    scopus 로고
    • Cotranslational membrane protein biogenesis at the endoplasmic reticulum
    • Alder, N.N.; Johnson, A.E. Cotranslational membrane protein biogenesis at the endoplasmic reticulum. J. Biol. Chem., 2004, 279(22), 22787-22790.
    • (2004) J. Biol. Chem , vol.279 , Issue.22 , pp. 22787-22790
    • Alder, N.N.1    Johnson, A.E.2
  • 72
    • 4644356464 scopus 로고    scopus 로고
    • Membrane-protein integration and the role of the translocation channel
    • Rapoport, T.A.; Goder, V.; Heinrich, S.U.; Matlack, K.E.S. Membrane-protein integration and the role of the translocation channel. Trends Cell Biol., 2004, 14(10), 568-575.
    • (2004) Trends Cell Biol , vol.14 , Issue.10 , pp. 568-575
    • Rapoport, T.A.1    Goder, V.2    Heinrich, S.U.3    Matlack, K.E.S.4
  • 75
    • 24644490119 scopus 로고    scopus 로고
    • Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
    • Nilsson, J.; Persson, B.; von Heijne, G. Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins, 2005, 60(4), 606-616.
    • (2005) Proteins , vol.60 , Issue.4 , pp. 606-616
    • Nilsson, J.1    Persson, B.2    von Heijne, G.3
  • 76
    • 0026716643 scopus 로고
    • Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
    • von Heijne, G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol., 1992, 225(2), 487-494.
    • (1992) J. Mol. Biol , vol.225 , Issue.2 , pp. 487-494
    • von Heijne, G.1
  • 77
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones, D.T.; Taylor, W.R.; Thornton, J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, 1994, 33(10), 3038-3049.
    • (1994) Biochemistry , vol.33 , Issue.10 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 79
    • 4944242989 scopus 로고    scopus 로고
    • An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins
    • Martelli, P.L.; Fariselli, P.; Casadio, R. An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics, 2003, 19(Suppl 1), i205-i211.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Martelli, P.L.1    Fariselli, P.2    Casadio, R.3
  • 80
    • 0037633968 scopus 로고    scopus 로고
    • Predicting the topology of transmembrane helical proteins using mean burial propensity and a hiddenMarkov-model-based method
    • Zhou, H.; Zhou, Y. Predicting the topology of transmembrane helical proteins using mean burial propensity and a hiddenMarkov-model-based method. Protein Sci., 2003, 12(7), 1547-1555.
    • (2003) Protein Sci , vol.12 , Issue.7 , pp. 1547-1555
    • Zhou, H.1    Zhou, Y.2
  • 81
    • 9544252210 scopus 로고    scopus 로고
    • A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction
    • Zheng, W.J.; Spassov, V.Z.; Yan, L.; Flook, P.K.; Szalma, S. A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. Comput. Biol. Chem., 2004, 28(4), 265-274.
    • (2004) Comput. Biol. Chem , vol.28 , Issue.4 , pp. 265-274
    • Zheng, W.J.1    Spassov, V.Z.2    Yan, L.3    Flook, P.K.4    Szalma, S.5
  • 82
    • 33947417295 scopus 로고    scopus 로고
    • A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins
    • Fariselli, P.; Martelli, P.L.; Casadio, R. A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics, 2005, 6(Suppl.) 4, S12.
    • (2005) BMC Bioinformatics , vol.6 , Issue.4
    • Fariselli, P.1    Martelli, P.L.2    Casadio, R.3
  • 83
    • 48249151108 scopus 로고    scopus 로고
    • OCTOPUS: Improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
    • Viklund, H.; Elofsson, A. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics, 2008, 24(15), 1662-1668.
    • (2008) Bioinformatics , vol.24 , Issue.15 , pp. 1662-1668
    • Viklund, H.1    Elofsson, A.2
  • 84
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • Jones, D.T. Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics, 2007, 23(5), 538-544.
    • (2007) Bioinformatics , vol.23 , Issue.5 , pp. 538-544
    • Jones, D.T.1
  • 85
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner, L. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 1989, 77(2), 257-286.
    • (1989) Proc. IEEE , vol.77 , Issue.2 , pp. 257-286
    • Rabiner, L.1
  • 86
    • 0036132818 scopus 로고    scopus 로고
    • Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies
    • Ikeda, M.; Arai, M.; Lao, D.M.; Shimizu, T. Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies. In Silico Biol., 2002, 2(1), 19-33.
    • (2002) In Silico Biol , vol.2 , Issue.1 , pp. 19-33
    • Ikeda, M.1    Arai, M.2    Lao, D.M.3    Shimizu, T.4
  • 87
    • 0034899781 scopus 로고    scopus 로고
    • Evaluation of methods for the prediction of membrane spanning regions
    • Möller, S.; Croning, M.D.; Apweiler, R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 2001, 17(7), 646-653.
    • (2001) Bioinformatics , vol.17 , Issue.7 , pp. 646-653
    • Möller, S.1    Croning, M.D.2    Apweiler, R.3
  • 88
    • 0041620242 scopus 로고    scopus 로고
    • BPROMPT: A consensus server for membrane protein prediction
    • Taylor, P.D.; Attwood, T.K.; Flower, D.R. BPROMPT: A consensus server for membrane protein prediction. Nucleic Acids Res., 2003, 31(13), 3698-3700.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3698-3700
    • Taylor, P.D.1    Attwood, T.K.2    Flower, D.R.3
  • 89
    • 0842308529 scopus 로고    scopus 로고
    • ConPred_elite: A highly reliable approach to transmembrane topology predication
    • Xia, J.; Ikeda, M.; Shimizu, T. ConPred_elite: a highly reliable approach to transmembrane topology predication. Comput. Biol. Chem., 2004, 28(1), 51-60.
    • (2004) Comput. Biol. Chem , vol.28 , Issue.1 , pp. 51-60
    • Xia, J.1    Ikeda, M.2    Shimizu, T.3
  • 90
    • 3242891271 scopus 로고    scopus 로고
    • ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability
    • Arai, M.; Mitsuke, H.; Ikeda, M.; Xia, J.; Kikuchi, T.; Satake, M.; Shimizu, T. ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res., 2004, 32(Web Server issue), W390-W393.
    • (2004) Nucleic Acids Res , vol.32 , Issue.Web Server issue
    • Arai, M.1    Mitsuke, H.2    Ikeda, M.3    Xia, J.4    Kikuchi, T.5    Satake, M.6    Shimizu, T.7
  • 91
    • 0034672544 scopus 로고    scopus 로고
    • Consensus predictions of membrane protein topology
    • Nilsson, J.; Persson, B.; von Heijne, G. Consensus predictions of membrane protein topology. FEBS Lett., 2000, 486(3), 267-269.
    • (2000) FEBS Lett , vol.486 , Issue.3 , pp. 267-269
    • Nilsson, J.1    Persson, B.2    von Heijne, G.3
  • 92
    • 0036891703 scopus 로고    scopus 로고
    • Prediction of partial membrane protein topologies using a consensus approach
    • Nilsson, J.; Persson, B.; Von Heijne, G. Prediction of partial membrane protein topologies using a consensus approach. Protein Sci., 2002, 11(12), 2974-2980.
    • (2002) Protein Sci , vol.11 , Issue.12 , pp. 2974-2980
    • Nilsson, J.1    Persson, B.2    von Heijne, G.3
  • 93
    • 0034495418 scopus 로고    scopus 로고
    • A collection of well characterised integral membrane proteins
    • Möller, S.; Kriventseva, E.V.; Apweiler, R. A collection of well characterised integral membrane proteins. Bioinformatics, 2000, 16(12), 1159-1160.
    • (2000) Bioinformatics , vol.16 , Issue.12 , pp. 1159-1160
    • Möller, S.1    Kriventseva, E.V.2    Apweiler, R.3
  • 94
    • 0037249645 scopus 로고    scopus 로고
    • TMPDB: A database of experimentally-characterized transmembrane topologies
    • Ikeda, M.; Arai, M.; Okuno, T.; Shimizu, T. TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res., 2003, 31(1), 406-409.
    • (2003) Nucleic Acids Res , vol.31 , Issue.1 , pp. 406-409
    • Ikeda, M.1    Arai, M.2    Okuno, T.3    Shimizu, T.4
  • 95
    • 0042121119 scopus 로고    scopus 로고
    • Static benchmarking of membrane helix predictions
    • Kernytsky, A.; Rost, B. Static benchmarking of membrane helix predictions. Nucleic Acids Res., 2003, 31(13), 3642-3644.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3642-3644
    • Kernytsky, A.1    Rost, B.2
  • 96
    • 0034888209 scopus 로고    scopus 로고
    • A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: The OrienTM algorithm
    • Liakopoulos, T.D.; Pasquier, C.; Hamodrakas, S.J. A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. Protein Eng., 2001, 14(6), 387-390.
    • (2001) Protein Eng , vol.14 , Issue.6 , pp. 387-390
    • Liakopoulos, T.D.1    Pasquier, C.2    Hamodrakas, S.J.3
  • 97
    • 0344406716 scopus 로고    scopus 로고
    • Reliability measures for membrane protein topology prediction algorithms
    • Melén, K.; Krogh, A.; von Heijne, G. Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol., 2003, 327(3), 735-744.
    • (2003) J. Mol. Biol , vol.327 , Issue.3 , pp. 735-744
    • Melén, K.1    Krogh, A.2    von Heijne, G.3
  • 99
    • 33747879895 scopus 로고    scopus 로고
    • A combinatorial pattern discovery approach for the prediction of membrane dipping (reentrant) loops
    • Lasso, G.; Antoniw, J.F.; Mullins, J.G.L. A combinatorial pattern discovery approach for the prediction of membrane dipping (reentrant) loops. Bioinformatics, 2006, 22(14), e290-e297.
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Lasso, G.1    Antoniw, J.F.2    Mullins, J.G.L.3
  • 101
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusnády, G.E.; Simon, I. The HMMTOP transmembrane topology prediction server. Bioinformatics, 2001, 17(9), 849-850.
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 849-850
    • Tusnády, G.E.1    Simon, I.2
  • 102
    • 22244451035 scopus 로고    scopus 로고
    • Improved membrane protein topology prediction by domain assignments
    • Bernsel, A.; von Heijne, G. Improved membrane protein topology prediction by domain assignments. Protein Sci., 2005, 14(7), 1723-1728.
    • (2005) Protein Sci , vol.14 , Issue.7 , pp. 1723-1728
    • Bernsel, A.1    von Heijne, G.2
  • 103
    • 33645297088 scopus 로고    scopus 로고
    • The use of functional domains to improve transmembrane protein topology prediction
    • Xu, E.W.; Kearney, P.; Brown, D.G. The use of functional domains to improve transmembrane protein topology prediction. J. Bioinform. Comput. Biol., 2006, 4(1), 109-123.
    • (2006) J. Bioinform. Comput. Biol , vol.4 , Issue.1 , pp. 109-123
    • Xu, E.W.1    Kearney, P.2    Brown, D.G.3
  • 104
    • 33847155026 scopus 로고    scopus 로고
    • Algorithms for incorporating prior topological information in HMMs: Application to transmembrane proteins
    • Bagos, P.G.; Liakopoulos, T.D.; Hamodrakas, S.J. Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics, 2006, 7, 189.
    • (2006) BMC Bioinformatics , vol.7 , pp. 189
    • Bagos, P.G.1    Liakopoulos, T.D.2    Hamodrakas, S.J.3
  • 106
    • 0038701655 scopus 로고    scopus 로고
    • Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions
    • Kim, H.; Melén, K.; von Heijne, G. Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J. Biol. Chem., 2003, 278(12), 10208-10213.
    • (2003) J. Biol. Chem , vol.278 , Issue.12 , pp. 10208-10213
    • Kim, H.1    Melén, K.2    von Heijne, G.3
  • 107
    • 0037022611 scopus 로고    scopus 로고
    • Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis
    • Drew, D.; Sjöstrand, D.; Nilsson, J.; Urbig, T.; Chin, C.; de Gier, J.; von Heijne, G. Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc. Natl. Acad. Sci. USA, 2002, 99(5), 2690-2695.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , Issue.5 , pp. 2690-2695
    • Drew, D.1    Sjöstrand, D.2    Nilsson, J.3    Urbig, T.4    Chin, C.5    de Gier, J.6    von Heijne, G.7
  • 109
    • 24044436844 scopus 로고    scopus 로고
    • Experimentally constrained topology models for 51,208 bacterial inner membrane proteins
    • Granseth, E.; Daley, D.O.; Rapp, M.; Melén, K.; von Heijne, G. Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J. Mol. Biol., 2005, 352(3), 489-494.
    • (2005) J. Mol. Biol , vol.352 , Issue.3 , pp. 489-494
    • Granseth, E.1    Daley, D.O.2    Rapp, M.3    Melén, K.4    von Heijne, G.5
  • 111
    • 33747843417 scopus 로고    scopus 로고
    • Localizome: A server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
    • Lee, S.; Lee, B.; Jang, I.; Kim, S.; Bhak, J. Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Nucleic Acids Res., 2006, 34(Web Server issue), W99-W103.
    • (2006) Nucleic Acids Res , vol.34 , Issue.Web Server issue
    • Lee, S.1    Lee, B.2    Jang, I.3    Kim, S.4    Bhak, J.5
  • 112
    • 45449101527 scopus 로고    scopus 로고
    • TOPDOM: Database of domains and motifs with conservative location in transmembrane proteins
    • Tusnády, G.E.; Kalmár, L.; Hegyi, H.; Tompa, P.; Simon, I. TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. Bioinformatics, 2008, 24(12), 1469-1470.
    • (2008) Bioinformatics , vol.24 , Issue.12 , pp. 1469-1470
    • Tusnády, G.E.1    Kalmár, L.2    Hegyi, H.3    Tompa, P.4    Simon, I.5
  • 113
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin, E.; von Heijne, G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci., 1998, 7(4), 1029-1038.
    • (1998) Protein Sci , vol.7 , Issue.4 , pp. 1029-1038
    • Wallin, E.1    von Heijne, G.2
  • 114
    • 0037132511 scopus 로고    scopus 로고
    • Reliability of transmembrane predictions in whole-genome data
    • Käll, L.; Sonnhammer, E.L.L. Reliability of transmembrane predictions in whole-genome data. FEBS Lett., 2002, 532(3), 415-418.
    • (2002) FEBS Lett , vol.532 , Issue.3 , pp. 415-418
    • Käll, L.1    Sonnhammer, E.L.L.2
  • 116
    • 2942567744 scopus 로고    scopus 로고
    • Global analysis of predicted proteomes: Functional adaptation of physical properties
    • Knight, C.G.; Kassen, R.; Hebestreit, H.; Rainey, P.B. Global analysis of predicted proteomes: functional adaptation of physical properties. Proc. Natl. Acad. Sci. USA, 2004, 101(22), 8390-8395.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.22 , pp. 8390-8395
    • Knight, C.G.1    Kassen, R.2    Hebestreit, H.3    Rainey, P.B.4
  • 117
    • 0027509460 scopus 로고
    • Analysis of the topology of a membrane protein by using a minimum number of alkaline phosphatase fusions
    • Boyd, D.; Traxler, B.; Beckwith, J. Analysis of the topology of a membrane protein by using a minimum number of alkaline phosphatase fusions. J. Bacteriol., 1993, 175(2), 553-556.
    • (1993) J. Bacteriol , vol.175 , Issue.2 , pp. 553-556
    • Boyd, D.1    Traxler, B.2    Beckwith, J.3
  • 118
    • 0023883641 scopus 로고
    • Genetic analysis of the membrane insertion and topology of MalF, a cytoplasmic membrane protein of Escherichia coli
    • Froshauer, S.; Green, G.N.; Boyd, D.; McGovern, K.; Beckwith, J. Genetic analysis of the membrane insertion and topology of MalF, a cytoplasmic membrane protein of Escherichia coli. J. Mol. Biol., 1988, 200(3), 501-511.
    • (1988) J. Mol. Biol , vol.200 , Issue.3 , pp. 501-511
    • Froshauer, S.1    Green, G.N.2    Boyd, D.3    McGovern, K.4    Beckwith, J.5
  • 119
    • 0025053613 scopus 로고
    • Beta-lactamase as a probe of membrane protein assembly and protein export
    • Broome-Smith, J.K.; Tadayyon, M.; Zhang, Y. Beta-lactamase as a probe of membrane protein assembly and protein export. Mol. Microbiol., 1990, 4(10), 1637-1644.
    • (1990) Mol. Microbiol , vol.4 , Issue.10 , pp. 1637-1644
    • Broome-Smith, J.K.1    Tadayyon, M.2    Zhang, Y.3
  • 120
    • 0035815754 scopus 로고    scopus 로고
    • Membrane topology and function of Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endoplasmic reticulum degradation
    • Deak, P.M.; Wolf, D.H. Membrane topology and function of Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endoplasmic reticulum degradation. J. Biol. Chem., 2001, 276(14), 10663-10669.
    • (2001) J. Biol. Chem , vol.276 , Issue.14 , pp. 10663-10669
    • Deak, P.M.1    Wolf, D.H.2
  • 121
    • 0028902788 scopus 로고
    • Transmembrane helices predicted at 95% accuracy
    • Rost, B.; Casadio, R.; Fariselli, P.; Sander, C. Transmembrane helices predicted at 95% accuracy. Protein Sci., 1995, 4(3), 521-533.
    • (1995) Protein Sci , vol.4 , Issue.3 , pp. 521-533
    • Rost, B.1    Casadio, R.2    Fariselli, P.3    Sander, C.4
  • 122
    • 0030038634 scopus 로고    scopus 로고
    • Topology prediction for helical transmembrane proteins at 86% accuracy
    • Rost, B.; Fariselli, P.; Casadio, R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci., 1996, 5(8), 1704-1718.
    • (1996) Protein Sci , vol.5 , Issue.8 , pp. 1704-1718
    • Rost, B.1    Fariselli, P.2    Casadio, R.3
  • 123
    • 0035109170 scopus 로고    scopus 로고
    • MPtopo: A database of membrane protein topology
    • Jayasinghe, S.; Hristova, K.; White, S.H. MPtopo: A database of membrane protein topology. Protein Sci., 2001, 10(2), 455-458.
    • (2001) Protein Sci , vol.10 , Issue.2 , pp. 455-458
    • Jayasinghe, S.1    Hristova, K.2    White, S.H.3
  • 124
    • 3042621274 scopus 로고    scopus 로고
    • The progress of membrane protein structure determination
    • White, S.H. The progress of membrane protein structure determination. Protein Sci., 2004, 13(7), 1948-1949.
    • (2004) Protein Sci , vol.13 , Issue.7 , pp. 1948-1949
    • White, S.H.1
  • 125
    • 38649141141 scopus 로고    scopus 로고
    • Estimating the length of transmembrane helices using Z-coordinate predictions
    • Papaloukas, C.; Granseth, E.; Viklund, H.; Elofsson, A. Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci., 2008, 17(2), 271-278.
    • (2008) Protein Sci , vol.17 , Issue.2 , pp. 271-278
    • Papaloukas, C.1    Granseth, E.2    Viklund, H.3    Elofsson, A.4
  • 127
    • 33744490360 scopus 로고    scopus 로고
    • Positioning of proteins in membranes: A computational approach
    • Lomize, A.L.; Pogozheva, I.D.; Lomize, M.A.; Mosberg, H.I. Positioning of proteins in membranes: a computational approach. Protein Sci., 2006, 15(6), 1318-1333.
    • (2006) Protein Sci , vol.15 , Issue.6 , pp. 1318-1333
    • Lomize, A.L.1    Pogozheva, I.D.2    Lomize, M.A.3    Mosberg, H.I.4
  • 128
    • 33644873454 scopus 로고    scopus 로고
    • TCDB: The Transporter Classification Database for membrane transport protein analyses and information
    • Saier, M.H.; Tran, C.V.; Barabote, R.D. TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res., 2006, 34(Database issue), D181-D186.
    • (2006) Nucleic Acids Res , vol.34 , Issue.Database issue
    • Saier, M.H.1    Tran, C.V.2    Barabote, R.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.