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Volumn 81, Issue 7, 2013, Pages 1127-1140

Simultaneous prediction of protein secondary structure and transmembrane spans

Author keywords

Membrane proteins; Protein structure prediction; ProteinDataBank; Secondary structure prediction; Transmembrane span prediction

Indexed keywords

MEMBRANE PROTEIN;

EID: 84879411265     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24258     Document Type: Article
Times cited : (52)

References (56)
  • 1
    • 79851516036 scopus 로고    scopus 로고
    • Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination
    • Kazmier K, Alexander NS, Meiler J, Mchaourab HS. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination. J Struct Biol 2011;173:549-557.
    • (2011) J Struct Biol , vol.173 , pp. 549-557
    • Kazmier, K.1    Alexander, N.S.2    Meiler, J.3    Mchaourab, H.S.4
  • 3
    • 0028158628 scopus 로고
    • Phd-an Automatic Mail Server for Protein Secondary Structure Prediction
    • Rost B, Sander C, Schneider R. Phd-an Automatic Mail Server for Protein Secondary Structure Prediction. Comput Appl Biosci 1994;10:53-60.
    • (1994) Comput Appl Biosci , vol.10 , pp. 53-60
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 4
    • 0029889988 scopus 로고    scopus 로고
    • Phd-: predicting one-dimensional protein structure by profile-based neural networks
    • Rost B. Phd-: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol 1996;266:525-539.
    • (1996) Methods Enzymol , vol.266 , pp. 525-539
    • Rost, B.1
  • 5
    • 13444266488 scopus 로고    scopus 로고
    • A simple and fast secondary structure prediction method using hidden neural networks
    • Lin K, Simossis VA, Taylor WR, Heringa J. A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 2005;21:152-159.
    • (2005) Bioinformatics , vol.21 , pp. 152-159
    • Lin, K.1    Simossis, V.A.2    Taylor, W.R.3    Heringa, J.4
  • 6
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 7
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000;16:404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 9
    • 0142027795 scopus 로고    scopus 로고
    • Coupled prediction of protein secondary and tertiary structure
    • Meiler J, Baker D. Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci USA 2003;100:12105-12110.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12105-12110
    • Meiler, J.1    Baker, D.2
  • 10
    • 0035789525 scopus 로고    scopus 로고
    • Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks
    • Meiler J, Muller M, Zeidler A, Schmaschke F. Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks. J Mol Model 2001;7:360-369.
    • (2001) J Mol Model , vol.7 , pp. 360-369
    • Meiler, J.1    Muller, M.2    Zeidler, A.3    Schmaschke, F.4
  • 11
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L, Sander C. Mapping the protein universe. Science 1996;273:595-603.
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 12
    • 0027169638 scopus 로고
    • Improved prediction of protein secondary structure by use of sequence profiles and neural networks
    • Rost B, Sander C. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci USA 1993;90:7558-7562.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 7558-7562
    • Rost, B.1    Sander, C.2
  • 13
    • 0028158628 scopus 로고
    • PHD-an automatic mail server for protein secondary structure prediction
    • Rost B, Sander C, Schneider R. PHD-an automatic mail server for protein secondary structure prediction. Comput Appl Biosci 1994;10:53-60.
    • (1994) Comput Appl Biosci , vol.10 , pp. 53-60
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 14
    • 0000448982 scopus 로고
    • Prediction of protein antigenic determinants from amino acid sequences
    • Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 1981;78:3824-3828.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 3824-3828
    • Hopp, T.P.1    Woods, K.R.2
  • 15
    • 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 1986;15:321-353.
    • (1986) Annu Rev Biophys Biophys Chem , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 16
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
    • Wimley WC, Creamer TP, White SH. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 1996;35:5109-5124.
    • (1996) Biochemistry , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 17
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: physical principles
    • White SH, Wimley WC. Membrane protein folding and stability: physical principles. Ann Rev Biophys Biomol Struct 1999;28:319-365.
    • (1999) Ann Rev Biophys Biomol Struct , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 20
    • 79959928058 scopus 로고    scopus 로고
    • Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers
    • Moon CP, Fleming KG. Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci USA 2011;108:10174-10177.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 10174-10177
    • Moon, C.P.1    Fleming, K.G.2
  • 21
    • 0018784438 scopus 로고
    • Surface and inside volumes in globular proteins
    • Janin J. Surface and inside volumes in globular proteins. Nature 1979;277:491-492.
    • (1979) Nature , vol.277 , pp. 491-492
    • Janin, J.1
  • 22
    • 0037231039 scopus 로고    scopus 로고
    • A knowledge-based scale for amino acid membrane propensity
    • Punta M, Maritan A. A knowledge-based scale for amino acid membrane propensity. Proteins 2003;50:114-121.
    • (2003) Proteins , vol.50 , pp. 114-121
    • Punta, M.1    Maritan, A.2
  • 23
    • 4444382786 scopus 로고    scopus 로고
    • A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins
    • Beuming T, Weinstein H. A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics 2004;20:1822-1835.
    • (2004) Bioinformatics , vol.20 , pp. 1822-1835
    • Beuming, T.1    Weinstein, H.2
  • 24
    • 33846399142 scopus 로고    scopus 로고
    • E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices
    • Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF. E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices. J Mol Biol 2007;366:436-448.
    • (2007) J Mol Biol , vol.366 , pp. 436-448
    • Senes, A.1    Chadi, D.C.2    Law, P.B.3    Walters, R.F.4    Nanda, V.5    Degrado, W.F.6
  • 26
    • 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 1982;157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 28
    • 0021977590 scopus 로고
    • Amino acid side-chain partition energies and distribution of residues in soluble proteins
    • Guy HR. Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophys J 1985;47:61-70.
    • (1985) Biophys J , vol.47 , pp. 61-70
    • Guy, H.R.1
  • 29
    • 0029738872 scopus 로고    scopus 로고
    • Experimentally determined hydrophobicity scale for proteins at membrane interfaces
    • Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 1996;3:842-848.
    • (1996) Nat Struct Biol , vol.3 , pp. 842-848
    • Wimley, W.C.1    White, S.H.2
  • 30
    • 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;24:1662-1668.
    • (2008) Bioinformatics , vol.24 , pp. 1662-1668
    • Viklund, H.1    Elofsson, A.2
  • 31
    • 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 EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305:567-580.
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 32
    • 18744403991 scopus 로고    scopus 로고
    • An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
    • Kahsay RY, Gao G, Liao L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics 2005;21:1853-1858.
    • (2005) Bioinformatics , vol.21 , pp. 1853-1858
    • Kahsay, R.Y.1    Gao, G.2    Liao, L.3
  • 33
    • 67649472570 scopus 로고    scopus 로고
    • Transmembrane protein topology prediction using support vector machines
    • Nugent T, Jones DT. Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics 2009;10.
    • (2009) BMC Bioinformatics , pp. 10
    • Nugent, T.1    Jones, D.T.2
  • 34
    • 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 JX, 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:W390-W393.
    • (2004) Nucleic 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
  • 35
    • 0842308529 scopus 로고    scopus 로고
    • ConPred_elite: a highly reliable approach to transmembrane topology predication
    • Xia JX, Ikeda M, Shimizu T. ConPred_elite: a highly reliable approach to transmembrane topology predication. Comput Biol Chem 2004;28:51-60.
    • (2004) Comput Biol Chem , vol.28 , pp. 51-60
    • Xia, J.X.1    Ikeda, M.2    Shimizu, T.3
  • 36
    • 1842688091 scopus 로고    scopus 로고
    • Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins
    • Gromiha MM, Ahmad S, Suwa M. Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. J Comput Chem 2004;25:762-767.
    • (2004) J Comput Chem , vol.25 , pp. 762-767
    • Gromiha, M.M.1    Ahmad, S.2    Suwa, M.3
  • 38
    • 33747846585 scopus 로고    scopus 로고
    • PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins
    • Bigelow H, Rost B. PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res 2006;34:W186-W188.
    • (2006) Nucleic Acids Res , vol.34
    • Bigelow, H.1    Rost, B.2
  • 39
    • 0041620432 scopus 로고    scopus 로고
    • The PredictProtein server
    • Rost B, Liu J. The PredictProtein server. Nucl Acids Res 2003;31:3300-3304.
    • (2003) Nucl Acids Res , vol.31 , pp. 3300-3304
    • Rost, B.1    Liu, J.2
  • 40
    • 79955605443 scopus 로고    scopus 로고
    • TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues
    • Singh NK, Goodman A, Walter P, Helms V, Hayat S. TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues. Biochim Biophys Acta 2011;1814:664-670.
    • (2011) Biochim Biophys Acta , vol.1814 , pp. 664-670
    • Singh, N.K.1    Goodman, A.2    Walter, P.3    Helms, V.4    Hayat, S.5
  • 41
    • 10244252813 scopus 로고    scopus 로고
    • Transmembrane proteins in the Protein Data Bank: identification and classification
    • Tusnady GE, Dosztanyi Z, Simon I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics 2004;20:2964-2972.
    • (2004) Bioinformatics , vol.20 , pp. 2964-2972
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 42
    • 13444280419 scopus 로고    scopus 로고
    • PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank
    • Tusnady GE, Dosztanyi Z, Simon I. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 2005;33:D275-D278.
    • (2005) Nucleic Acids Res , vol.33
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 43
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang GL, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.L.1    Dunbrack, R.L.2
  • 44
    • 23144438711 scopus 로고    scopus 로고
    • PISCES: recent improvements to a PDB sequence culling server
    • Wang G, Dunbrack RL, Jr. PISCES: recent improvements to a PDB sequence culling server. Nucleic acids research 2005;33:W94-W98.
    • (2005) Nucleic acids research , vol.33
    • Wang, G.1    Dunbrack, R.L.2
  • 45
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 47
    • 84879414629 scopus 로고    scopus 로고
    • PDBTM: Protein Data Bank of Transmembrane Proteins. Available at: Accessed on February 14
    • PDBTM: Protein Data Bank of Transmembrane Proteins. Available at:http://pdbtm.enzim.hu/. Accessed on February 14, 2013.
    • (2013)
  • 48
    • 79956294243 scopus 로고    scopus 로고
    • Crystal structure of the Vibrio cholerae cytolysin heptamer reveals common features among disparate pore-forming toxins
    • De S, Olson R. Crystal structure of the Vibrio cholerae cytolysin heptamer reveals common features among disparate pore-forming toxins. Proc Natl Acad Sci USA 2011;108:7385-7390.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 7385-7390
    • De, S.1    Olson, R.2
  • 51
    • 0033615736 scopus 로고    scopus 로고
    • The mechanism of membrane insertion for a cholesterol-dependent cytolysin: a novel paradigm for pore-forming toxins
    • Shatursky O, Heuck AP, Shepard LA, Rossjohn J, Parker MW, Johnson AE, Tweten RK. The mechanism of membrane insertion for a cholesterol-dependent cytolysin: a novel paradigm for pore-forming toxins. Cell 1999;99:293-299.
    • (1999) Cell , vol.99 , pp. 293-299
    • Shatursky, O.1    Heuck, A.P.2    Shepard, L.A.3    Rossjohn, J.4    Parker, M.W.5    Johnson, A.E.6    Tweten, R.K.7
  • 52
    • 17444405610 scopus 로고    scopus 로고
    • Structural basis of pore formation by the bacterial toxin pneumolysin
    • Tilley SJ, Orlova EV, Gilbert RJ, Andrew PW, Saibil HR. Structural basis of pore formation by the bacterial toxin pneumolysin. Cell 2005;121:247-256.
    • (2005) Cell , vol.121 , pp. 247-256
    • Tilley, S.J.1    Orlova, E.V.2    Gilbert, R.J.3    Andrew, P.W.4    Saibil, H.R.5
  • 53
    • 0030447720 scopus 로고    scopus 로고
    • Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore
    • Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouaux JE. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 1996;274:1859-1866.
    • (1996) Science , vol.274 , pp. 1859-1866
    • Song, L.1    Hobaugh, M.R.2    Shustak, C.3    Cheley, S.4    Bayley, H.5    Gouaux, J.E.6
  • 54
    • 0032932083 scopus 로고    scopus 로고
    • Crystal structure of staphylococcal LukF delineates conformational changes accompanying formation of a transmembrane channel
    • Olson R, Nariya H, Yokota K, Kamio Y, Gouaux E. Crystal structure of staphylococcal LukF delineates conformational changes accompanying formation of a transmembrane channel. Nat Struct Biol 1999;6:134-140.
    • (1999) Nat Struct Biol , vol.6 , pp. 134-140
    • Olson, R.1    Nariya, H.2    Yokota, K.3    Kamio, Y.4    Gouaux, E.5
  • 55
    • 0030587932 scopus 로고    scopus 로고
    • An alpha to beta conformational switch in EF-Tu
    • Abel K, Yoder MD, Hilgenfeld R, Jurnak F. An alpha to beta conformational switch in EF-Tu. Structure 1996;4:1153-1159.
    • (1996) Structure , vol.4 , pp. 1153-1159
    • Abel, K.1    Yoder, M.D.2    Hilgenfeld, R.3    Jurnak, F.4


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