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Volumn 59, Issue 4, 2005, Pages 828-839

High accuracy prediction of β-turns and their types using propensities and multiple alignments

Author keywords

turn type prediction; turns; Multiple alignments COUDES; Prediction; Propensities

Indexed keywords

AMINO ACID;

EID: 18844414326     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20461     Document Type: Article
Times cited : (99)

References (43)
  • 1
    • 0034327349 scopus 로고    scopus 로고
    • Prediction of tight turns and their types in proteins
    • Chou KG. 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.G.1
  • 2
    • 0028566270 scopus 로고
    • A revised set of potentials for beta-turn formation in proteins
    • Hutchinson EG, Thornton JM. A revised set of potentials for beta-turn formation in proteins. Protein Sci 1994;3:2207-2216.
    • (1994) Protein Sci , vol.3 , pp. 2207-2216
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 3
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981;34:167-339.
    • (1981) Adv Protein Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 6
    • 0037648871 scopus 로고    scopus 로고
    • Design of beta-turn based therapeutic agents
    • Kee KS, Jois SD. Design of beta-turn based therapeutic agents. Curr Pharm Des 2003;9:1209-1224.
    • (2003) Curr Pharm Des , vol.9 , pp. 1209-1224
    • Kee, K.S.1    Jois, S.D.2
  • 7
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of beta-hairpin formation
    • Munoz V, Thompson PA, Hofrichter J, Eaton WA. Folding dynamics and mechanism of beta-hairpin formation. Nature 1997;390: 196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 8
    • 0034635340 scopus 로고    scopus 로고
    • Beta-Hairpin stability and folding: Molecular dynamics studies of the first beta-hairpin of tendamistat
    • Bonvin AM, van Gunsteren WF. beta-Hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. J Mol Biol 2000;296:255-268.
    • (2000) J Mol Biol , vol.296 , pp. 255-268
    • Bonvin, A.M.1    Van Gunsteren, W.F.2
  • 9
    • 0015114095 scopus 로고
    • Folding of polypeptide chains in proteins: A proposed mechanism for folding
    • Lewis PN, Momany FA, Scheraga HA. Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc Natl Acad Sci USA 1971;68:2293-2297.
    • (1971) Proc Natl Acad Sci USA , vol.68 , pp. 2293-2297
    • Lewis, P.N.1    Momany, F.A.2    Scheraga, H.A.3
  • 10
    • 0015967881 scopus 로고
    • Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins
    • Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 1974;13:211-222.
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 11
    • 0015987426 scopus 로고
    • Prediction of protein conformation
    • Chou PY, Fasman GD. Prediction of protein conformation. Biochemistry 1974;13:222-245.
    • (1974) Biochemistry , vol.13 , pp. 222-245
    • Chou, P.Y.1    Fasman, G.D.2
  • 12
    • 0017709445 scopus 로고
    • Beta-turns in proteins
    • Chou PY, Fasman GD. Beta-turns in proteins. J Mol Biol 1977;115: 135-175.
    • (1977) J Mol Biol , vol.115 , pp. 135-175
    • Chou, P.Y.1    Fasman, G.D.2
  • 13
    • 0018476871 scopus 로고
    • Prediction of beta-turns
    • Chou PY, Fasman GD. Prediction of beta-turns. Biophys J 1979;26: 367-373.
    • (1979) Biophys J , vol.26 , pp. 367-373
    • Chou, P.Y.1    Fasman, G.D.2
  • 14
    • 0017873321 scopus 로고
    • Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
    • Garnier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978;120:97-120.
    • (1978) J Mol Biol , vol.120 , pp. 97-120
    • Garnier, J.1    Osguthorpe, D.J.2    Robson, B.3
  • 15
    • 0017798828 scopus 로고
    • Prediction of chain turns in globular proteins on a hydrophobic basis
    • Rose GD. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature 1978;272:586-590.
    • (1978) Nature , vol.272 , pp. 586-590
    • Rose, G.D.1
  • 16
    • 0024279235 scopus 로고
    • Analysis and prediction of the different types of beta-turn in proteins
    • Wilmot CM, Thornton JM. Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol 1988;203:221-232.
    • (1988) J Mol Biol , vol.203 , pp. 221-232
    • Wilmot, C.M.1    Thornton, J.M.2
  • 17
    • 0025113022 scopus 로고
    • Beta-turns and their distortions: A proposed new nomenclature
    • Wilmot CM, Thornton JM. Beta-turns and their distortions: a proposed new nomenclature. Protein Eng 1990;3:479-493.
    • (1990) Protein Eng , vol.3 , pp. 479-493
    • Wilmot, C.M.1    Thornton, J.M.2
  • 18
    • 0033752859 scopus 로고    scopus 로고
    • Beta- and gamma-turns in proteins revisited: A new set of amino acid turn-type dependent positional preferences and potentials
    • Guruprasad K, Rajkumar S. Beta- and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials. J Biosci 2000;25:143-156.
    • (2000) J Biosci , vol.25 , pp. 143-156
    • Guruprasad, K.1    Rajkumar, S.2
  • 19
    • 0031149431 scopus 로고    scopus 로고
    • Prediction of beta-turns in proteins by 1-4 and 2-3 correlation model
    • Zhang CT, Chou KC. Prediction of beta-turns in proteins by 1-4 and 2-3 correlation model. Biopolymers 1997;41:673-702.
    • (1997) Biopolymers , vol.41 , pp. 673-702
    • Zhang, C.T.1    Chou, K.C.2
  • 20
    • 0030808140 scopus 로고    scopus 로고
    • Classification and prediction of beta-turn types
    • Chou KC, Blinn JR. Classification and prediction of beta-turn types. J Protein Chem 1997;16:575-595.
    • (1997) J Protein Chem , vol.16 , pp. 575-595
    • Chou, K.C.1    Blinn, J.R.2
  • 21
    • 0030963006 scopus 로고    scopus 로고
    • Prediction of beta-turns
    • Chou KC. Prediction of beta-turns. J Pept Res 1997;49:120-144.
    • (1997) J Pept Res , vol.49 , pp. 120-144
    • Chou, K.C.1
  • 22
    • 0024412170 scopus 로고
    • Prediction of beta-turns in proteins using neural networks
    • McGregor MJ, Flores TP, Sternberg MJ. Prediction of beta-turns in proteins using neural networks. Protein Eng 1989;2:521-526.
    • (1989) Protein Eng , vol.2 , pp. 521-526
    • McGregor, M.J.1    Flores, T.P.2    Sternberg, M.J.3
  • 23
    • 0032900496 scopus 로고    scopus 로고
    • Prediction of the location and type of beta-turns in proteins using neural networks
    • Shepherd AJ, Gorse D, Thornton JM. Prediction of the location and type of beta-turns in proteins using neural networks. Protein Sci 1999;8:1045-1055.
    • (1999) Protein Sci , vol.8 , pp. 1045-1055
    • Shepherd, A.J.1    Gorse, D.2    Thornton, J.M.3
  • 24
    • 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
  • 25
    • 0036855904 scopus 로고    scopus 로고
    • An evaluation of beta-turn prediction methods
    • Kaur H, Raghava GP. An evaluation of beta-turn prediction methods. Bioinformatics 2002;18:1508-1514.
    • (2002) Bioinformatics , vol.18 , pp. 1508-1514
    • Kaur, H.1    Raghava, G.P.2
  • 26
    • 0033933636 scopus 로고    scopus 로고
    • Cascaded multiple classifiers for secondary structure prediction
    • Ouali M, King RD. Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000;9:1162-1176.
    • (2000) Protein Sci , vol.9 , pp. 1162-1176
    • Ouali, M.1    King, R.D.2
  • 27
    • 0037372098 scopus 로고    scopus 로고
    • Prediction of beta-turns in proteins from multiple alignment using neural network
    • Kaur H, Raghava GP. Prediction of beta-turns in proteins from multiple alignment using neural network. Protein Sci 2003;12:627-634.
    • (2003) Protein Sci , vol.12 , pp. 627-634
    • Kaur, H.1    Raghava, G.P.2
  • 28
    • 0345832339 scopus 로고    scopus 로고
    • Protein beta-turn prediction using nearest-neighbor method
    • Kim S. Protein beta-turn prediction using nearest-neighbor method. Bioinformatics 2004;20:40-44.
    • (2004) Bioinformatics , vol.20 , pp. 40-44
    • Kim, S.1
  • 29
    • 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
  • 30
  • 31
    • 8844252295 scopus 로고    scopus 로고
    • A neural network method for prediction of beta-turn types in proteins using evolutionary information
    • Kaur KS, Raghava GP. A neural network method for prediction of beta-turn types in proteins using evolutionary information. Bioinformatics 2004;16:2751-2758.
    • (2004) Bioinformatics , vol.16 , pp. 2751-2758
    • Kaur, K.S.1    Raghava, G.P.2
  • 33
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
    • (1994) Protein Sci , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 34
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF - A program to identify and analyze structural motifs in proteins
    • Hutchinson EG, Thornton JM. PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci 1996;5: 212-220.
    • (1996) Protein Sci , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 35
    • 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
  • 37
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein 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 protein 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
  • 38
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: An overview
    • Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000;16:412-424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.4    Nielsen, H.5
  • 39
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Mathews BW. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975;405:442-451.
    • (1975) Biochim Biophys Acta , vol.405 , pp. 442-451
    • Mathews, B.W.1
  • 40
    • 2942541294 scopus 로고    scopus 로고
    • Use of a structural alphabet for analysis of short loops connecting repetitive structures
    • Fourrier L, Benros C, de Brevern AG. Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinformatics 2004;5:58.
    • (2004) BMC Bioinformatics , vol.5 , pp. 58
    • Fourrier, L.1    Benros, C.2    De Brevern, A.G.3
  • 41
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
    • (1993) J Mol Biol , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 42
    • 0036467068 scopus 로고    scopus 로고
    • Alignments grow, secondary structure prediction improves
    • Przybylski D, Rost B. Alignments grow, secondary structure prediction improves. Proteins 2002;46:197-205.
    • (2002) Proteins , vol.46 , pp. 197-205
    • Przybylski, D.1    Rost, B.2
  • 43
    • 1442349113 scopus 로고    scopus 로고
    • Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information
    • Kaur H, Raghava GP. Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information. Proteins 2004;55:83-90.
    • (2004) Proteins , vol.55 , pp. 83-90
    • Kaur, H.1    Raghava, G.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.