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Volumn 8, Issue 1, 2010, Pages 39-57

TOPTMH: Topology predictor for transmembrane α-helices

Author keywords

Classification; Hidden Markov model; Membrane protein; Secondary structure; Support vector machines

Indexed keywords

MEMBRANE PROTEIN;

EID: 77951614017     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720010004501     Document Type: Article
Times cited : (5)

References (38)
  • 1
    • 0001911218 scopus 로고    scopus 로고
    • State-of-the-art in membrane protein prediction
    • Chen CP, Rost B, State-of-the-art in membrane protein prediction, Appl Bioinform 1(1):21-35, 2002.
    • (2002) Appl Bioinform , vol.1 , Issue.1 , pp. 21-35
    • Chen, C.P.1    Rost, B.2
  • 2
    • 0037020329 scopus 로고    scopus 로고
    • Drug design strategies for targeting g-protein-coupled receptors
    • Klabunde T, Hessler G, Drug design strategies for targeting g-protein-coupled receptors, ChemBioChem 3:928-944, 2002.
    • (2002) ChemBioChem , vol.3 , pp. 928-944
    • Klabunde, T.1    Hessler, G.2
  • 3
    • 33745698481 scopus 로고    scopus 로고
    • A limited universe of membrane protein families and folds
    • Jul
    • Oberai A, Ihm Y, Kim S, Bowie JU, A limited universe of membrane protein families and folds, Protein Sci 15(7):1723-1734, Jul 2006.
    • (2006) Protein Sci , vol.15 , Issue.7 , pp. 1723-1734
    • Oberai, A.1    Ihm, Y.2    Kim, S.3    Bowie, J.U.4
  • 5
    • 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 7(4):1029-1038, 1998.
    • (1998) Protein Sci , vol.7 , Issue.4 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 6
    • 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 225(2):487-494, 1992.
    • (1992) J Mol Biol , vol.225 , Issue.2 , pp. 487-494
    • Von Heijne, G.1
  • 7
    • 0030038634 scopus 로고    scopus 로고
    • Topology prediction for helical transmembrane proteins at 86 accuracy
    • Aug
    • Rost B, Fariselli P, Casadio R, Topology prediction for helical transmembrane proteins at 86 accuracy, Protein Sci 5(8):1704-1718, Aug 1996.
    • (1996) Protein Sci , vol.5 , Issue.8 , pp. 1704-1718
    • Rost, B.1    Fariselli, P.2    Casadio, R.3
  • 8
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • Jones DT, Improving the accuracy of transmembrane protein topology prediction using evolutionary information, Bioinformatics 23(5):538-544, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.5 , pp. 538-544
    • Jones, D.T.1
  • 9
    • 39749179168 scopus 로고    scopus 로고
    • Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function
    • Feb
    • Lo A, Chiu H-S, Sung T-Y, Lyu P-C, Hsu W-L, Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function, J Proteome Res 7(2):487-496, Feb 2008.
    • (2008) J Proteome Res , vol.7 , Issue.2 , pp. 487-496
    • Lo, A.1    Chiu, H.-S.2    Sung, T.-Y.3    Lyu, P.-C.4    Hsu, W.-L.5
  • 10
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF, A simple method for displaying the hydropathic character of a protein, J Mol Biol 157(1):105-132, 1982.
    • (1982) J Mol Biol , vol.157 , Issue.1 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 11
    • 0037633968 scopus 로고    scopus 로고
    • Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method
    • Zhou H, Zhou Y, Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-markov-model-based method, Protein Sci 12:1547-1555, 2003.
    • (2003) Protein Sci , vol.12 , pp. 1547-1555
    • Zhou, H.1    Zhou, Y.2
  • 13
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • May
    • Käll L, Krogh A, Sonnhammer ELL, A combined transmembrane topology and signal peptide prediction method, J Mol Biol 338(5):1027-1036, May 2004.
    • (2004) J Mol Biol , vol.338 , Issue.5 , pp. 1027-1036
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 14
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner LR, A tutorial on hidden markov models and selected applications in speech recognition, in Proc IEEE Vol, 77, pp. 257-286, 1989.
    • (1989) Proc IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 16
    • 47349085903 scopus 로고    scopus 로고
    • Frmsdpred: Predicting local rmsd between structural fragments using sequence information
    • Aug
    • Rangwala H, Karypis G, frmsdpred: Predicting local rmsd between structural fragments using sequence information, Proteins 72(3):1005-1018, Aug 2008.
    • (2008) Proteins , vol.72 , Issue.3 , pp. 1005-1018
    • Rangwala, H.1    Karypis, G.2
  • 17
    • 33746267388 scopus 로고    scopus 로고
    • Yasspp: Better kernels and coding schemes lead to improvements in protein secondary structure prediction
    • Aug
    • Karypis G, Yasspp: Better kernels and coding schemes lead to improvements in protein secondary structure prediction, Proteins 64(3):575-586, Aug 2006.
    • (2006) Proteins , vol.64 , Issue.3 , pp. 575-586
    • Karypis, G.1
  • 19
    • 0042121119 scopus 로고    scopus 로고
    • Static benchmarking of membrane helix predictions
    • Jul
    • Kernytsky A, Rost B, Static benchmarking of membrane helix predictions, Nucleic Acids Res 31(13):3642-3644, Jul 2003.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3642-3644
    • Kernytsky, A.1    Rost, B.2
  • 21
    • 34547571030 scopus 로고    scopus 로고
    • The UniProt Consortium, The universal protein resource (uniprot)
    • The UniProt Consortium, The universal protein resource (uniprot). Nucleic Acids Res 35:D193-D197, 2007.
    • (2007) Nucleic Acids Res , vol.35
  • 22
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman DM, Steitz TA, Goldman A, Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins, Annu Rev Biophys Biophys Chem 15:321-353, 1986.
    • (1986) Annu Rev Biophys Biophys Chem , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 23
    • 34247614946 scopus 로고    scopus 로고
    • Formation of transmembrane helices in vivo - Is hydrophobicity all that matters?
    • von Heijne G, Formation of transmembrane helices in vivo - Is hydrophobicity all that matters? J Gen Physiol 129(5):353-356, 2007.
    • (2007) J Gen Physiol , vol.129 , Issue.5 , pp. 353-356
    • Von Heijne, G.1
  • 25
    • 0037132511 scopus 로고    scopus 로고
    • Reliability of transmembrane predictions in whole-genome data
    • Dec
    • Käll L, Erik Sonnhammer LL, Reliability of transmembrane predictions in whole-genome data, FEBS Lett 532(3):415-418, Dec 2002.
    • (2002) FEBS Lett , vol.532 , Issue.3 , pp. 415-418
    • Käll, L.1    Erik Sonnhammer, L.L.2
  • 26
    • 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 76:125-140, 2007.
    • (2007) Annu Rev Biochem , vol.76 , pp. 125-140
    • Elofsson, A.1    Von Heijne, G.2
  • 28
    • 0042121119 scopus 로고    scopus 로고
    • Static benchmarking of membrane helix predictions
    • Kernytsky A, Rost B, Static benchmarking of membrane helix predictions, Nucleic Aci ds Res 31(13):3642-3644, 2003.
    • (2003) Nucleic Aci Ds Res , vol.31 , Issue.13 , pp. 3642-3644
    • Kernytsky, A.1    Rost, B.2
  • 30
    • 0035109170 scopus 로고    scopus 로고
    • Mptopo: A database of membrane protein topology
    • Feb
    • Jayasinghe S, Hristova K, White SH, Mptopo: A database of membrane protein topology, Protein Sci 10(2):455-458, Feb 2001.
    • (2001) Protein Sci , vol.10 , Issue.2 , pp. 455-458
    • Jayasinghe, S.1    Hristova, K.2    White, S.H.3
  • 31
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Jul
    • Li W, Godzik A, Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics 22(13):1658-1659, Jul 2006.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 32
    • 0034808117 scopus 로고    scopus 로고
    • Comparing function and structure between entire proteomes
    • Liu J, Rost B, Comparing function and structure between entire proteomes, Protein Sci 10:1970-1979, 2001.
    • (2001) Protein Sci , vol.10 , pp. 1970-1979
    • Liu, J.1    Rost, B.2
  • 33
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Jan
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL, Predicting transmembrane protein topology with a hidden markov model: Application to complete genomes, J Mol Biol 305(3):567-580, Jan 2001.
    • (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
  • 34
    • 0034786532 scopus 로고    scopus 로고
    • The hmmtop transmembrane topology prediction server
    • Sep
    • Tusnády GE, Simon I, The hmmtop transmembrane topology prediction server, Bioin-formatics 17(9):849-850, Sep 2001.
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 849-850
    • Tusnády, G.E.1    Simon, I.2
  • 35
    • 0030759333 scopus 로고    scopus 로고
    • Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method
    • Jun
    • Cserzö 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 10(6):673-676, Jun 1997.
    • (1997) Protein Eng , vol.10 , Issue.6 , pp. 673-676
    • Cserzö, M.1    Wallin, E.2    Simon, I.3    Von Heijne, G.4    Elofsson, A.5
  • 36
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman DM, Steitz TA, Goldman A, Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins, Annu Rev Biophys Biophys Chem 15:321-353, 1986.
    • (1986) Annu Rev Biophys Biophys Chem , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 37
    • 0031826040 scopus 로고    scopus 로고
    • Sosui: Classification and secondary structure prediction system for membrane proteins
    • Hirokawa T, Boon-Chieng S, Mitaku S, Sosui: Classification and secondary structure prediction system for membrane proteins, Bioinformatics 14:378-379, 1998.
    • (1998) Bioinformatics , vol.14 , pp. 378-379
    • Hirokawa, T.1    Boon-Chieng, S.2    Mitaku, S.3
  • 38
    • 33746361201 scopus 로고    scopus 로고
    • Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: Application to complete genomes
    • Aug
    • 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 361(3):591-603, Aug 2006.
    • (2006) J Mol Biol , vol.361 , Issue.3 , pp. 591-603
    • Viklund, H.1    Granseth, E.2    Elofsson, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.