메뉴 건너뛰기




Volumn 320, Issue , 2013, Pages 152-158

Probing the protein space for extending the detection of weak homology folds

Author keywords

Protein fold; Protein motif; Remote homology; Structural bioinformatics; Structure prediction

Indexed keywords

LYASE;

EID: 84872470906     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.12.005     Document Type: Article
Times cited : (5)

References (52)
  • 3
    • 84863859936 scopus 로고    scopus 로고
    • Levinthal's question revisited, and answered
    • Ben-Naim A. Levinthal's question revisited, and answered. J. Biomol. Struct. Dyn. 2012, 30:113-124.
    • (2012) J. Biomol. Struct. Dyn. , vol.30 , pp. 113-124
    • Ben-Naim, A.1
  • 4
    • 79953093817 scopus 로고    scopus 로고
    • A discriminative method for family-based proteinremote homology detection that combines inductive logic programming and propositional models
    • Bernardes J.S., Carbone A., Zaverucha G. A discriminative method for family-based proteinremote homology detection that combines inductive logic programming and propositional models. BMC Bioinformatics 2011, 12:83-95.
    • (2011) BMC Bioinformatics , vol.12 , pp. 83-95
    • Bernardes, J.S.1    Carbone, A.2    Zaverucha, G.3
  • 5
    • 30444446362 scopus 로고    scopus 로고
    • Protein-structure prediction by recombination of fragments
    • Bujnicki J.M. Protein-structure prediction by recombination of fragments. ChemBioChem 2006, 7:19-27.
    • (2006) ChemBioChem , vol.7 , pp. 19-27
    • Bujnicki, J.M.1
  • 8
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C., Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986, 5:823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 9
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • Chothia C. Proteins. One thousand families for the molecular biologist. Nature 1992, 357:543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 10
    • 77949360269 scopus 로고    scopus 로고
    • Template-based protein modeling: recent methodological advances
    • Daga P.R., Patel R.Y., Doerksen R.J. Template-based protein modeling: recent methodological advances. Curr. Top. Med. Chem. 2010, 10:84-94.
    • (2010) Curr. Top. Med. Chem. , vol.10 , pp. 84-94
    • Daga, P.R.1    Patel, R.Y.2    Doerksen, R.J.3
  • 11
    • 0043268757 scopus 로고    scopus 로고
    • Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update
    • Du P., Andrec M., Levy R.M. Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng. 2003, 16:407-414.
    • (2003) Protein Eng. , vol.16 , pp. 407-414
    • Du, P.1    Andrec, M.2    Levy, R.M.3
  • 14
    • 37149056501 scopus 로고    scopus 로고
    • A historical perspective of template-based protein structure prediction
    • Guo J.T., Ellrott J.T.K., Xu Y. A historical perspective of template-based protein structure prediction. Methods Mol. Biol. 2008, 413:3-42.
    • (2008) Methods Mol. Biol. , vol.413 , pp. 3-42
    • Guo, J.T.1    Ellrott, J.T.K.2    Xu, Y.3
  • 16
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: extension and analysis of the basic method
    • Hughey R., Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci. 1996, 12:95-107.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 17
    • 84943817322 scopus 로고
    • Error detecting and error correcting codes
    • Hamming R.W. Error detecting and error correcting codes. Bell Syst. Tech. J. 1950, 26:147-160.
    • (1950) Bell Syst. Tech. J. , vol.26 , pp. 147-160
    • Hamming, R.W.1
  • 18
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones A.T., Thirup S. Using known substructures in protein model building and crystallography. EMBO J. 1986, 5:819-822.
    • (1986) EMBO J. , vol.5 , pp. 819-822
    • Jones, A.T.1    Thirup, S.2
  • 20
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus K., Barrett C., Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998, 14:846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 21
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • Kolodny R., Koehl P., Guibas L., Levitt M. Small libraries of protein fragments model native protein structures accurately. J. Mol. Biol. 2002, 323:297-307.
    • (2002) J. Mol. Biol. , vol.323 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 22
    • 48449099769 scopus 로고    scopus 로고
    • Domain Hierarchy and closed loops (DHcL): a server for exploring hierarchy of protein domain structure
    • Koczyk G., Berezovsky I.N. Domain Hierarchy and closed loops (DHcL): a server for exploring hierarchy of protein domain structure. Nucleic Acid Res. 2008, 36:239-245.
    • (2008) Nucleic Acid Res. , vol.36 , pp. 239-245
    • Koczyk, G.1    Berezovsky, I.N.2
  • 23
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., Doolittle R. 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.2
  • 24
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: a case study using the Phyre server
    • Kelley L.A., Sternberg M.J. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4:363-371.
    • (2009) Nat. Protoc. , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 25
    • 79957979204 scopus 로고    scopus 로고
    • Comparative modeling: the state of the art and protein drug target structure prediction
    • Liu T., Tang G.W., Capriotti E. Comparative modeling: the state of the art and protein drug target structure prediction. Comb. Chem. High Throughput Screen. 2011, 14:532-547.
    • (2011) Comb. Chem. High Throughput Screen. , vol.14 , pp. 532-547
    • Liu, T.1    Tang, G.W.2    Capriotti, E.3
  • 26
    • 0035783055 scopus 로고    scopus 로고
    • On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?
    • Lupas A.N., Ponting C.P., Russell R.B. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?. J. Struct. Biol. 2001, 134:191-203.
    • (2001) J. Struct. Biol. , vol.134 , pp. 191-203
    • Lupas, A.N.1    Ponting, C.P.2    Russell, R.B.3
  • 27
    • 0031765884 scopus 로고    scopus 로고
    • Hydropathy profile alignment: a tool to search for structural homologues of membrane proteins
    • Lolkema J.S., Slotboom D. Hydropathy profile alignment: a tool to search for structural homologues of membrane proteins. FEMS Microb. Rev. 1998, 22:305-322.
    • (1998) FEMS Microb. Rev. , vol.22 , pp. 305-322
    • Lolkema, J.S.1    Slotboom, D.2
  • 28
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247:536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 29
    • 55749113550 scopus 로고    scopus 로고
    • Profile comparer: a program for scoring and aligning profile hidden Markov models
    • Madera M. Profile comparer: a program for scoring and aligning profile hidden Markov models. Bioinformatics 2008, 24:2630-2631.
    • (2008) Bioinformatics , vol.24 , pp. 2630-2631
    • Madera, M.1
  • 30
    • 80054685109 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP)-round IX
    • Moult J., Fidelis K., Kryshtafovych A., Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-round IX. Proteins 2011, 79:1-5.
    • (2011) Proteins , vol.79 , pp. 1-5
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Tramontano, A.4
  • 32
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970, 48:443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 34
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo C.A., Jones D.T., Thornton J.M. Protein superfamilies and domain superfolds. Nature 1994, 372:631-634.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 35
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson W.R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 1990, 183:63-98.
    • (1990) Methods Enzymol. , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 36
    • 0033004893 scopus 로고    scopus 로고
    • Predicting the protein folding nucleus from a sequence
    • Poupon A., Mornon J.P. Predicting the protein folding nucleus from a sequence. FEBS Lett. 1999, 452:283-289.
    • (1999) FEBS Lett. , vol.452 , pp. 283-289
    • Poupon, A.1    Mornon, J.P.2
  • 37
    • 34548806425 scopus 로고    scopus 로고
    • Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone
    • Reid A.J., Yeats C., Orengo C.A. Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics 2007, 23:2353-2360.
    • (2007) Bioinformatics , vol.23 , pp. 2353-2360
    • Reid, A.J.1    Yeats, C.2    Orengo, C.A.3
  • 38
    • 0030878180 scopus 로고    scopus 로고
    • A protein designed by binary patterning of polar and nonpolar amino acids displays native-like properties
    • Roy S., Ratnaswamy G., Boice J.A., Fairman R., McLendon G., Hecht M.H. A protein designed by binary patterning of polar and nonpolar amino acids displays native-like properties. J. Am. Chem. Soc. 1997, 119:5302-5306.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 5302-5306
    • Roy, S.1    Ratnaswamy, G.2    Boice, J.A.3    Fairman, R.4    McLendon, G.5    Hecht, M.H.6
  • 39
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 40
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm
    • Skolnick J., Kihara D., Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Protein 2004, 56:502-518.
    • (2004) Protein , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 41
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 43
    • 0035055990 scopus 로고    scopus 로고
    • Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues
    • Schwartz R., Istrail S., King J. Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues. Protein Sci. 2001, 10:1023-1031.
    • (2001) Protein Sci. , vol.10 , pp. 1023-1031
    • Schwartz, R.1    Istrail, S.2    King, J.3
  • 44
    • 67849119587 scopus 로고    scopus 로고
    • COMPASS server for homology detection: improved statistical accuracy, speed and functionality
    • Sadreyev R.I., Tang M., Kim B., Grishin N.V. COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acid Res. 2009, 37:90-94.
    • (2009) Nucleic Acid Res. , vol.37 , pp. 90-94
    • Sadreyev, R.I.1    Tang, M.2    Kim, B.3    Grishin, N.V.4
  • 45
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 2001, 307:1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 46
    • 0039080152 scopus 로고
    • Do exons code for structural or functional units in proteins?
    • Traut T.W. Do exons code for structural or functional units in proteins?. Proc. Natl. Acad. Sci. USA 1988, 85:2944-2948.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2944-2948
    • Traut, T.W.1
  • 47
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res. 1994, 22:4673-4680.
    • (1994) Nucleic Acid Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 48
    • 0032594959 scopus 로고    scopus 로고
    • An overview of statistical learning theory
    • Vapnik V.N. An overview of statistical learning theory. IEEE Trans. Neural Networks 1999, 10:988-999.
    • (1999) IEEE Trans. Neural Networks , vol.10 , pp. 988-999
    • Vapnik, V.N.1
  • 49
    • 65349160977 scopus 로고    scopus 로고
    • Structural bioinformatics: from the sequence to structure and function
    • Wiltgen M. Structural bioinformatics: from the sequence to structure and function. Curr. Bioinformatics 2009, 4:54-87.
    • (2009) Curr. Bioinformatics , vol.4 , pp. 54-87
    • Wiltgen, M.1
  • 50
    • 64549115839 scopus 로고    scopus 로고
    • Protein structure prediction: when is it useful?
    • Zhang Y. Protein structure prediction: when is it useful?. Curr. Opin. Struct. Biol. 2009, 19:145-155.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 145-155
    • Zhang, Y.1
  • 51
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • Zhang Y. Progress and challenges in protein structure prediction. Curr. Opin. Struct. Biol. 2008, 18:342-348.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 342-348
    • Zhang, Y.1
  • 52
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on TM-score
    • Zhang Y., Skolnick J. TM-align: a protein structure alignment algorithm based on TM-score. Nucleic Acid Res. 2005, 33:2302-2309.
    • (2005) Nucleic Acid Res. , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.