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Volumn 5, Issue , 2004, Pages

Use of a structural alphabet for analysis of short loops connecting repetitive structures

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN APPROACHES; DIFFERENT STRUCTURE; PROTEIN FRAGMENTS; REGULAR SECONDARY STRUCTURES; REPETITIVE STRUCTURE; SECONDARY STRUCTURES; SPECIFIC LEARNING; STRUCTURAL ALPHABET;

EID: 2942541294     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-58     Document Type: Article
Times cited : (57)

References (45)
  • 1
    • 0004792589 scopus 로고
    • Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains
    • Pauling L, Corey RB: Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains. Proc Natl Acad Sci USA 1951, 37: 235-240.
    • (1951) Proc. Natl. Acad. Sci. USA , vol.37 , pp. 235-240
    • Pauling, L.1    Corey, R.B.2
  • 2
    • 76549238253 scopus 로고
    • The Pleated Sheet, A New Layer Configuration of Polypeptide Chains
    • Pauling L, Corey RB: The Pleated Sheet, A New Layer Configuration of Polypeptide Chains. Proc Natl Acad Sci USA 1951, 37: 251-256.
    • (1951) Proc. Natl. Acad. Sci. USA , vol.37 , pp. 251-256
    • Pauling, L.1    Corey, R.B.2
  • 3
    • 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
  • 4
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure
    • Frishman D, Argos P: Knowledge-based protein secondary structure. Proteins 1995, 23: 566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 5
    • 0023927904 scopus 로고
    • Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure
    • Ridchards FM, Kundrot CE: Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 1988, 3: 71-84.
    • (1988) Proteins , vol.3 , pp. 71-84
    • Ridchards, F.M.1    Kundrot, C.E.2
  • 6
    • 0024821134 scopus 로고
    • Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis
    • Sklenar H, Etchebest C, Lavery R: Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 1989, 6: 46-60.
    • (1989) Proteins , vol.6 , pp. 46-60
    • Sklenar, H.1    Etchebest, C.2    Lavery, R.3
  • 8
    • 0027207221 scopus 로고
    • Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment
    • Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon, J-P: Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng. 1993, 6: 377-382.
    • (1993) Protein Eng. , vol.6 , pp. 377-382
    • Colloc'h, N.1    Etchebest, C.2    Thoreau, E.3    Henrissat, B.4    Mornon, J.-P.5
  • 9
    • 0035782925 scopus 로고    scopus 로고
    • Review: Protein secondary structure prediction continues to rise
    • Rost B: Review: protein secondary structure prediction continues to rise. J Struct Biol. 2001, 134: 204-218.
    • (2001) J. Struct. Biol. , vol.134 , pp. 204-218
    • Rost, B.1
  • 10
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of secondary structure in three and eight classes using recurrent neural networks and profiles
    • Pollastri G, Przybylski D, Rost B, Baldi, P: Improving the prediction of secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002, 47: 228-235.
    • (2002) Proteins , vol.47 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 11
    • 0034327349 scopus 로고    scopus 로고
    • Prediction of tight turns and their types in proteins
    • Chou KC: Prediction of tight turns and their types in proteins. Anal. Biochem. 2000, 286: 1-16.
    • (2000) Anal. Biochem. , vol.286 , pp. 1-16
    • Chou, K.C.1
  • 13
    • 0031991297 scopus 로고    scopus 로고
    • Structural classification of alphabetabeta and betabetaalpha supersecondary structure
    • Boutonnet NS, Kajava AV, Rooman, MJ: Structural classification of alphabetabeta and betabetaalpha supersecondary structure. Proteins 1998, 30: 193-212.
    • (1998) Proteins , vol.30 , pp. 193-212
    • Boutonnet, N.S.1    Kajava, A.V.2    Rooman, M.J.3
  • 14
    • 0033603394 scopus 로고    scopus 로고
    • New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification
    • Wojick J, Mornon J-P, Chomilier J: New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J Mol Biol. 1999, 289: 1469-1490.
    • (1999) J. Mol. Biol. , vol.289 , pp. 1469-1490
    • Wojick, J.1    Mornon, J.-P.2    Chomilier, J.3
  • 15
    • 0011735482 scopus 로고    scopus 로고
    • Beyond the secondary structures : The structural alphabets
    • Edited by Sangadai SG India: Trivandrum, Research Signpost
    • de Brevern AG, Camproux A-C, Hazout S, Etchebest C, Tuffery P: Beyond the secondary structures : the structural alphabets In Recent Adv In Prot Eng. Edited by Sangadai SG. Trivandrum, India: Research Signpost; 2001: 319-331.
    • (2001) Recent Adv. In Prot. Eng. , pp. 319-331
    • de Brevern, A.G.1    Camproux, A.-C.2    Hazout, S.3    Etchebest, C.4    Tuffery, P.5
  • 16
    • 2442484293 scopus 로고    scopus 로고
    • Evaluating local structure alphabets for protein structure prediction
    • PhD thesis. University of California, Computer Science Department
    • Karchin R: Evaluating local structure alphabets for protein structure prediction. PhD thesis. University of California, Computer Science Department; 2003.
    • (2003)
    • Karchin, R.1
  • 17
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • Kolodony 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
    • Kolodony, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 18
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motif
    • Bystroff C, Baker D: Prediction of local structure in proteins using a library of sequence-structure motif. J Mol Biol. 1998, 281: 565-577.
    • (1998) J. Mol. Biol. , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 19
    • 0034669774 scopus 로고    scopus 로고
    • Bayesian: Probabilistic approach for predicting backbone structures in terms of protein blocks
    • de Brevern AG, Etchebest C, Hazout S: Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 2000, 41: 271-287.
    • (2000) Proteins , vol.41 , pp. 271-287
    • de Brevern, A.G.1    Etchebest, C.2    Hazout, S.3
  • 20
    • 0035636385 scopus 로고    scopus 로고
    • Compacting local protein folds by a "Hybrid Protein Model"
    • de Brevern AG, Hazout S: Compacting local protein folds by a "Hybrid Protein Model". Theor Chem Acc. 2001, 106(1/2): 36-47.
    • (2001) Theor. Chem. Acc. , vol.106 , Issue.1-2 , pp. 36-47
    • de Brevern, A.G.1    Hazout, S.2
  • 21
    • 0037433050 scopus 로고    scopus 로고
    • 'Hybrid Protein Model' for optimally defining 3D protein structure fragments
    • de Brevern AG, Hazout, S: 'Hybrid Protein Model' for optimally defining 3D protein structure fragments. Bioinformatics 2003, 19: 345-353.
    • (2003) Bioinformatics , vol.19 , pp. 345-353
    • de Brevern, A.G.1    Hazout, S.2
  • 22
    • 2942530913 scopus 로고    scopus 로고
    • Hybrid Protein Model (HPM): A method for building a library of overlapping local structural prototypes. sensitivity study and improvements of the training
    • Benros C, de Brevern AG, Hazout S: Hybrid Protein Model (HPM): A method for building a library of overlapping local structural prototypes. sensitivity study and improvements of the training. IEEE Int Work. NNSP 2003, 1: 53-70.
    • (2003) IEEE Int. Work NNSP , vol.1 , pp. 53-70
    • Benros, C.1    de Brevern, A.G.2    Hazout, S.3
  • 23
    • 0036893073 scopus 로고    scopus 로고
    • Extension of a local backbone description using a structural alphabet. A new approach to the sequence-structure relationship
    • de Brevern, AG, Valadié H, Hazout S, Etchebest C: Extension of a local backbone description using a structural alphabet. A new approach to the sequence-structure relationship. Protein Sci. 2002, 11: 2871-2886.
    • (2002) Protein Sci. , vol.11 , pp. 2871-2886
    • de Brevern, A.G.1    Valadié, H.2    Hazout, S.3    Etchebest, C.4
  • 24
    • 0038278386 scopus 로고    scopus 로고
    • Hidden Markov models that use predicted local structure for fold recognition: Alphabets of protein backbone geometry
    • Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K: Hidden Markov models that use predicted local structure for fold recognition: alphabets of protein backbone geometry. Proteins 2003, 51: 504-514.
    • (2003) Proteins , vol.51 , pp. 504-514
    • Karchin, R.1    Cline, M.2    Mandel-Gutfreund, Y.3    Karplus, K.4
  • 25
    • 0026475673 scopus 로고
    • Detection of secondary structure elements in proteins by hydrophobic cluster analysis
    • Woodcock S, Mornon J-P, Henrissat B: Detection of secondary structure elements in proteins by hydrophobic cluster analysis. Prot Eng. 1992, 5: 629-635.
    • (1992) Prot. Eng. , vol.5 , pp. 629-635
    • Woodcock, S.1    Mornon, J.-P.2    Henrissat, B.3
  • 28
    • 0033106244 scopus 로고    scopus 로고
    • Evaluation and Improvement of multiple sequence methods for protein secondary structure prediction
    • Cuff J, Barton G: Evaluation and Improvement of multiple sequence methods for protein secondary structure prediction. Proteins 1999, 34: 508-519.
    • (1999) Proteins , vol.34 , pp. 508-519
    • Cuff, J.1    Barton, G.2
  • 29
    • 0033994775 scopus 로고    scopus 로고
    • HELANAL: A program to characterize helix geometry in proteins
    • Bansal M, Kumar S, Velavan R: HELANAL: a program to characterize helix geometry in proteins. J Bio Struct Dyn 2000, 17: 811-820.
    • (2000) J. Bio. Struct. Dyn. , vol.17 , pp. 811-820
    • Bansal, M.1    Kumar, S.2    Velavan, R.3
  • 30
    • 0036276409 scopus 로고    scopus 로고
    • Occurrence, conformational features and amino acid propensities for the pi-helix
    • Fodje MN, Al-Karadaghi S: Occurrence, conformational features and amino acid propensities for the pi-helix. Protein Eng. 2002, 15: 353-358.
    • (2002) Protein Eng. , vol.15 , pp. 353-358
    • Fodje, M.N.1    Al-Karadaghi, S.2
  • 31
    • 0043268757 scopus 로고    scopus 로고
    • Have we seen all structures corresponding to short protein fragments in the Protein Databank
    • Du P, Andrec M, Levy RM: Have we seen all structures corresponding to short protein fragments in the Protein Databank. Protein Eng. 2003, 16: 407-414.
    • (2003) Protein Eng. , vol.16 , pp. 407-414
    • Du, P.1    Andrec, M.2    Levy, R.M.3
  • 32
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A., Do RK, Sali A: Modeling of loops in protein structures. Protein Sci. 2000, 9: 1753-1773.
    • (2000) Protein Sci. , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 33
    • 0035588264 scopus 로고    scopus 로고
    • Exploring the use of a structural alphabet for a structural prediction of protein loops
    • Camproux A-C, de Brevern AG, Hazout S, Tuffery P: Exploring the use of a structural alphabet for a structural prediction of protein loops. Theor Chem Acc. 2001, 106(1/2): 28-35.
    • (2001) Theor. Chem. Acc. , vol.106 , Issue.1-2 , pp. 28-35
    • Camproux, A.-C.1    de Brevern, A.G.2    Hazout, S.3    Tuffery, P.4
  • 34
    • 0035237770 scopus 로고    scopus 로고
    • Novel approach to computer modeling of seven-helical transmembrane proteins: Current progress in the case of bacteriorhodopsin
    • Nikiforovich GV, Galaktionov S, Balodis J, Marshall GR: Novel approach to computer modeling of seven-helical transmembrane proteins: current progress in the case of bacteriorhodopsin. Acta Biochimic Polonica 2001, 48: 53-64.
    • (2001) Acta Biochimic Polonica , vol.48 , pp. 53-64
    • Nikiforovich, G.V.1    Galaktionov, S.2    Balodis, J.3    Marshall, G.R.4
  • 35
    • 0034870539 scopus 로고    scopus 로고
    • Ab initio modeling of small, medium, and large loops in proteins
    • Galaktionov S, Nikiforovich GV, Marshall GR: Ab initio modeling of small, medium, and large loops in proteins. Biopolymers 2001, 60: 153-168.
    • (2001) Biopolymers , vol.60 , pp. 153-168
    • Galaktionov, S.1    Nikiforovich, G.V.2    Marshall, G.R.3
  • 36
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein: Docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moghon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker, D: Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol. 2003, 331: 281-299.
    • (2003) J. Mol. Biol. , vol.331 , pp. 281-299
    • Gray, J.J.1    Moghon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 38
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • Kohonen T: Self-organized formation of topologically correct feature maps. Biol. Cybern. 1982, 43: 59-69.
    • (1982) Biol. Cybern. , vol.43 , pp. 59-69
    • Kohonen, T.1
  • 39
    • 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. Proc. of the IEEE 1989, 77: 257-285.
    • (1989) Proc. of the IEEE , vol.77 , pp. 257-285
    • Rabiner, L.R.1
  • 40
    • 0035172128 scopus 로고    scopus 로고
    • PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB)
    • Noguchi T, Matsuda H, Akiyama Y: PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). Nucleic Acids Res. 2001, 29: 219-220.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 219-220
    • Noguchi, T.1    Matsuda, H.2    Akiyama, Y.3
  • 42
    • 0000913086 scopus 로고
    • A fast algorithm for rendering space filling molecules pictures
    • Bacon DJ, Anderson WF: A fast algorithm for rendering space filling molecules pictures. J Mol Graph 1988, 6: 219-220.
    • (1988) J. Mol. Graph , vol.6 , pp. 219-220
    • Bacon, D.J.1    Anderson, W.F.2
  • 43
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt EA, Bacon DJ: Raster3D: Photorealistic molecular graphics. Methods in Enzym. 1997, 277: 505-524.
    • (1997) Methods in Enzym. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 44
    • 0026244229 scopus 로고
    • MOLSCRIPT: A Program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ: MOLSCRIPT: A Program to produce both detailed and schematic plots of protein structures. J Appl Cryst. 1991, 24: 946-950.
    • (1991) J. Appl. Cryst. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 45
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R, Billeter M, Wuthrich K: MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996, 14:51-55.
    • (1996) J. Mol. Graph , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3


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