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Volumn 1724, Issue 3, 2005, Pages 394-403

Hidden Markov Model-derived structural alphabet for proteins: The learning of protein local shapes captures sequence specificity

Author keywords

Hidden Markov Model; Protein structural organization; Sequence structure relationship; Structural alphabet

Indexed keywords

AMINO ACID; PROTEIN;

EID: 23144464777     PISSN: 03044165     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagen.2005.05.019     Document Type: Review
Times cited : (26)

References (32)
  • 2
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • T.A. Jones, and S. Thirup Using known substructures in protein model building and crystallography EMBO J. 5 1986 819 822
    • (1986) EMBO J. , vol.5 , pp. 819-822
    • Jones, T.A.1    Thirup, S.2
  • 4
    • 0024395940 scopus 로고
    • A 3D building blocks approach to analyzing and predicting structure of proteins
    • R. Unger, D. Harel, S. Wherland, and J.L. Sussman A 3D building blocks approach to analyzing and predicting structure of proteins Proteins 5 1989 355 373
    • (1989) Proteins , vol.5 , pp. 355-373
    • Unger, R.1    Harel, D.2    Wherland, S.3    Sussman, J.L.4
  • 5
    • 0025326949 scopus 로고
    • Automatic definition of recurrent local structure motifs in proteins
    • M.J. Rooman, J. Rodriguez, and S.J. Wodak Automatic definition of recurrent local structure motifs in proteins J. Mol. Biol. 213 1990 327 336
    • (1990) J. Mol. Biol. , vol.213 , pp. 327-336
    • Rooman, M.J.1    Rodriguez, J.2    Wodak, S.J.3
  • 6
    • 0026469666 scopus 로고
    • Generation of a substructure library for the description and classification of protein secondary structure: I. Overview of the methods and results
    • S.J. Prestrelski, A.L. Williams, and M.N. Liebman Generation of a substructure library for the description and classification of protein secondary structure: I. Overview of the methods and results Proteins 14 1992 430 439
    • (1992) Proteins , vol.14 , pp. 430-439
    • Prestrelski, S.J.1    Williams, A.L.2    Liebman, M.N.3
  • 7
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • M. Levitt Accurate modeling of protein conformation by automatic segment matching J. Mol. Biol. 226 1992 507 533
    • (1992) J. Mol. Biol. , vol.226 , pp. 507-533
    • Levitt, M.1
  • 8
    • 0029860175 scopus 로고    scopus 로고
    • Local structural motifs of proteins backbones are classified by self-organizing neural networks
    • J. Schuchhardt, G. Schneider, J. Reichelt, D. Schomburg, and P. Wrede Local structural motifs of proteins backbones are classified by self-organizing neural networks Protein Eng. 9 1996 833 842
    • (1996) Protein Eng. , vol.9 , pp. 833-842
    • Schuchhardt, J.1    Schneider, G.2    Reichelt, J.3    Schomburg, D.4    Wrede, P.5
  • 9
    • 0031052447 scopus 로고    scopus 로고
    • Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme
    • J.S. Fetrow, M.J. Palumbo, and G. Berg Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme Proteins 27 1997 249 271
    • (1997) Proteins , vol.27 , pp. 249-271
    • Fetrow, J.S.1    Palumbo, M.J.2    Berg, G.3
  • 10
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • C. Bystroff, and D. Baker Prediction of local structure in proteins using a library of sequence-structure motifs J. Mol. Biol. 281 1998 565 577
    • (1998) J. Mol. Biol. , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 11
    • 0034669774 scopus 로고    scopus 로고
    • Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
    • A.G. de Brevern, C. Etchebest, and S. Hazout Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks Proteins 41 2000 271 287
    • (2000) Proteins , vol.41 , pp. 271-287
    • De Brevern, A.G.1    Etchebest, C.2    Hazout, S.3
  • 12
    • 0034284383 scopus 로고    scopus 로고
    • Recurrent oligomers in proteins: An optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies
    • C. Micheletti, F. Seno, and A. Maritan Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies Proteins 40 2000 662 674
    • (2000) Proteins , vol.40 , pp. 662-674
    • Micheletti, C.1    Seno, F.2    Maritan, A.3
  • 13
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • R. Kolodny, P. Koehl, L. Guibas, and M. Levitt Small libraries of protein fragments model native protein structures accurately J. Mol. Biol. 323 2002 297 307
    • (2002) J. Mol. Biol. , vol.323 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 14
    • 0037339462 scopus 로고    scopus 로고
    • Protein fragment clustering and canonical local shapes
    • C.G. Hunter, and S. Subramaniam Protein fragment clustering and canonical local shapes Proteins 50 2003 580 588
    • (2003) Proteins , vol.50 , pp. 580-588
    • Hunter, C.G.1    Subramaniam, S.2
  • 15
    • 0033405214 scopus 로고    scopus 로고
    • Hidden Markov model approach for identifying the modular framework of the protein backbone
    • A.C. Camproux, P. Tuffery, J.P. Chevrolat, J.F. Boisvieux, and S. Hazout Hidden Markov model approach for identifying the modular framework of the protein backbone Protein Eng. 12 1999 1063 1073
    • (1999) Protein Eng. , vol.12 , pp. 1063-1073
    • Camproux, A.C.1    Tuffery, P.2    Chevrolat, J.P.3    Boisvieux, J.F.4    Hazout, S.5
  • 16
    • 2442592993 scopus 로고    scopus 로고
    • A hidden Markov model derived structural alphabet for proteins
    • A.C. Camproux, R. Gautier, and P. Tuffery A hidden Markov model derived structural alphabet for proteins J. Mol. Biol. 339 2004 591 605
    • (2004) J. Mol. Biol. , vol.339 , pp. 591-605
    • Camproux, A.C.1    Gautier, R.2    Tuffery, P.3
  • 17
    • 3242891058 scopus 로고    scopus 로고
    • SA-search: A web tool for protein structure mining based on structural alphabet
    • F. Guyon, A.C. Camproux, J. Hochez, and P. Tuffery SA-search: a web tool for protein structure mining based on structural alphabet Nar 32 2004 W545 W548
    • (2004) Nar , vol.32
    • Guyon, F.1    Camproux, A.C.2    Hochez, J.3    Tuffery, P.4
  • 18
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • L.R. Rabiner A tutorial on hidden Markov models and selected applications in speech recognition Proc. IEEE 77 1989 257 285
    • (1989) Proc. IEEE , vol.77 , pp. 257-285
    • Rabiner, L.R.1
  • 19
    • 0000353178 scopus 로고
    • A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains
    • L.E. Baum, T. Petrie, G. Soules, and N. Weiss A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains Ann. Math. Stat. 41 1970 164 171
    • (1970) Ann. Math. Stat. , vol.41 , pp. 164-171
    • Baum, L.E.1    Petrie, T.2    Soules, G.3    Weiss, N.4
  • 20
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • G. Schwartz Estimating the dimension of a model Ann. Stat. 6 1978 461 464
    • (1978) Ann. Stat. , vol.6 , pp. 461-464
    • Schwartz, G.1
  • 22
    • 0020122366 scopus 로고
    • Amino acid distribution in protein secondary structures
    • P. Argos, and J. Palau Amino acid distribution in protein secondary structures Int. J. Pept. Protein Res. 19 1982 380 393
    • (1982) Int. J. Pept. Protein Res. , vol.19 , pp. 380-393
    • Argos, P.1    Palau, J.2
  • 23
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of α-helices
    • J.S. Richardson, and D.C. Richardson Amino acid preferences for specific locations at the ends of α-helices Science 240 1988 1648 1652
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 24
    • 0024600819 scopus 로고
    • Protein structure analysis and development of databases
    • L. Presta Protein structure analysis and development of databases Protein Eng. 2 1989 395 397
    • (1989) Protein Eng. , vol.2 , pp. 395-397
    • Presta, L.1
  • 25
    • 0028173780 scopus 로고
    • Rule for α helix termination by glycine
    • R. Aurora, R. Srinivasan, and G.D. Rose Rule for α helix termination by glycine Science 264 1994 1126 1130
    • (1994) Science , vol.264 , pp. 1126-1130
    • Aurora, R.1    Srinivasan, R.2    Rose, G.D.3
  • 26
    • 0027986703 scopus 로고
    • Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices
    • J.W. Seales, R. Srinivasan, and G.D. Rose Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices Prot. Sci. 3 1994 1741 1745
    • (1994) Prot. Sci. , vol.3 , pp. 1741-1745
    • Seales, J.W.1    Srinivasan, R.2    Rose, G.D.3
  • 27
    • 0034604368 scopus 로고    scopus 로고
    • HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins
    • C. Bystroff, V. Thorsson, and D. Baker HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins J. Mol. Biol. 301 2000 173 190
    • (2000) J. Mol. Biol. , vol.301 , pp. 173-190
    • Bystroff, C.1    Thorsson, V.2    Baker, D.3
  • 28
    • 0043222570 scopus 로고    scopus 로고
    • Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA
    • C. Bystroff, and Y. Shao Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA Bioinformatics 18 2002 S54 S61
    • (2002) Bioinformatics , vol.18
    • Bystroff, C.1    Shao, Y.2
  • 29
    • 2442619694 scopus 로고    scopus 로고
    • Ab initio protein structure prediction of Casp III targets using ROSETTA
    • K. Simons, R. Bonneau, I. Ruczinki, and D. Baker Ab initio protein structure prediction of Casp III targets using ROSETTA Proteins 5 1999 355 373
    • (1999) Proteins , vol.5 , pp. 355-373
    • Simons, K.1    Bonneau, R.2    Ruczinki, I.3    Baker, D.4
  • 31
    • 0038278386 scopus 로고    scopus 로고
    • Hidden Markov models that use predicted local structure for fold recognition: Alphabets on backbone geometry
    • R. Karchin, M. Cline, Y. Mandel-Gutfreund, and K. Karplus Hidden Markov models that use predicted local structure for fold recognition: alphabets on backbone geometry Proteins 51 2003 504 514
    • (2003) Proteins , vol.51 , pp. 504-514
    • Karchin, R.1    Cline, M.2    Mandel-Gutfreund, Y.3    Karplus, K.4
  • 32
    • 0036893073 scopus 로고    scopus 로고
    • Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship
    • A.G. de Brevern, H. Valadie, S. Hazout, and C. Etchebest Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship Protein Sci. 11 2002 2871 2886
    • (2002) Protein Sci. , vol.11 , pp. 2871-2886
    • De Brevern, A.G.1    Valadie, H.2    Hazout, S.3    Etchebest, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.