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Volumn 12, Issue 2, 2003, Pages 288-295

Accurate and automated classification of protein secondary structure with PsiCSI

Author keywords

Chemical shifts; Neural networks; NMR; Secondary structure

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; ARTIFICIAL NEURAL NETWORK; AUTOMATION; CARBON NUCLEAR MAGNETIC RESONANCE; CLASSIFICATION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TECHNIQUE;

EID: 0037304379     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0222303     Document Type: Article
Times cited : (42)

References (32)
  • 2
    • 0033677333 scopus 로고    scopus 로고
    • The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data
    • Bailey-Kellogg, C., Widge, A., Kelley, J.J., Berardi, M.J., Bushweller, J.H., and Donald, B.R. 2000. The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. J. Comput. Biol. 7: 537-558.
    • (2000) J. Comput. Biol. , vol.7 , pp. 537-558
    • Bailey-Kellogg, C.1    Widge, A.2    Kelley, J.J.3    Berardi, M.J.4    Bushweller, J.H.5    Donald, B.R.6
  • 5
    • 0035487690 scopus 로고    scopus 로고
    • A tour of structural genomics
    • Brenner, S.E. 2001. A tour of structural genomics. Nat. Rev. Genet. 2: 801-809.
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 801-809
    • Brenner, S.E.1
  • 6
    • 0033757822 scopus 로고    scopus 로고
    • An overview of structural genomics
    • Burley, S.K. 2000. An overview of structural genomics. Nat. Struct. Biol. 7: 932-934.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 932-934
    • Burley, S.K.1
  • 7
    • 0015967881 scopus 로고
    • Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins
    • Chou, P.Y. and Fasman, G.D. 1974. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 13: 211-222.
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 8
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu, G., Delaglio, F., and Bax, A. 1999. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13: 289-302.
    • (1999) J. Biomol. NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 9
    • 0033106244 scopus 로고    scopus 로고
    • Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
    • Cuff, J.A. and Barton, G.J. 1999. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34: 508-519.
    • (1999) Proteins , vol.34 , pp. 508-519
    • Cuff, J.A.1    Barton, G.J.2
  • 10
    • 0034620764 scopus 로고    scopus 로고
    • Protein structure determiniation using molecular fragment replacement and NMR dipolar couplings
    • Delaglio, F., Kontaxis, G., and Bax, A. 2000. Protein structure determiniation using molecular fragment replacement and NMR dipolar couplings. J. Am. Chem. Soc. 122: 2142-2143.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2142-2143
    • Delaglio, F.1    Kontaxis, G.2    Bax, A.3
  • 12
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman, D. and Argos, P. 1995. Knowledge-based protein secondary structure assignment. Proteins 23: 566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 13
    • 0017873321 scopus 로고
    • Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
    • Garnier, J., Osguthorpe, D.J., and Robson, B. 1978. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120: 97-120.
    • (1978) J. Mol. Biol. , vol.120 , pp. 97-120
    • Garnier, J.1    Osguthorpe, D.J.2    Robson, B.3
  • 14
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on positionspecific scoring matrices
    • Jones, D.T. 1999. Protein secondary structure prediction based on positionspecific scoring matrices. J. Mol. Biol. 292: 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 15
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 16
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology. Applications to protein modeling
    • Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. 1994. Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol. 235: 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjolander, K.4    Haussler, D.5
  • 17
    • 0016162558 scopus 로고
    • Algorithms for prediction of α-helical and β-structural regions in globular proteins
    • Lim, V.I. 1974. Algorithms for prediction of α-helical and β-structural regions in globular proteins. J. Mol. Biol. 88: 873-894.
    • (1974) J. Mol. Biol. , vol.88 , pp. 873-894
    • Lim, V.I.1
  • 18
    • 0035923596 scopus 로고    scopus 로고
    • Structural genomics: An approach to the protein folding problem
    • Montelione, G.T. 2001. Structural genomics: An approach to the protein folding problem. Proc. Natl. Acad. Sci. 98: 13488-13489.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 13488-13489
    • Montelione, G.T.1
  • 19
    • 0034923123 scopus 로고    scopus 로고
    • Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data
    • Moseley, H.N., Monleon, D., and Montelione, G.T. 2001. Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol. 339: 91-108.
    • (2001) Methods Enzymol. , vol.339 , pp. 91-108
    • Moseley, H.N.1    Monleon, D.2    Montelione, G.T.3
  • 21
    • 0032613288 scopus 로고    scopus 로고
    • Ab initio folding of proteins using restraints derived from evolutionary information
    • Ortiz, A.R., Kolinski, A., Rotkiewicz, P., Ilkowski, B., and Skolnick, J. 1999. Ab initio folding of proteins using restraints derived from evolutionary information. Proteins 37: 177-185.
    • (1999) Proteins , vol.37 , pp. 177-185
    • Ortiz, A.R.1    Kolinski, A.2    Rotkiewicz, P.3    Ilkowski, B.4    Skolnick, J.5
  • 22
    • 0023927904 scopus 로고
    • Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure
    • Richards, F.M. and Kundrot, C.E. 1988. Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure. Proteins 3: 71-84.
    • (1988) Proteins , vol.3 , pp. 71-84
    • Richards, F.M.1    Kundrot, C.E.2
  • 23
    • 0037139549 scopus 로고    scopus 로고
    • De novo determination of protein backbone structure from residual dipolar couplings using rosetta
    • Rohl, C.A. and Baker, D. 2002. De novo determination of protein backbone structure from residual dipolar couplings using rosetta. J. Am. Chem. Soc. 124: 2723-2729.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 2723-2729
    • Rohl, C.A.1    Baker, D.2
  • 24
    • 0029889988 scopus 로고    scopus 로고
    • PHD: Predicting one-dimensional protein structure by profilebased neural networks
    • Rost, B. 1996. PHD: Predicting one-dimensional protein structure by profilebased neural networks. Methods Enzymol. 266: 525-539.
    • (1996) Methods Enzymol. , vol.266 , pp. 525-539
    • Rost, B.1
  • 25
    • 0035698737 scopus 로고    scopus 로고
    • EVA: Large-scale analysis of secondary structure prediction
    • Rost, B. and Eyrich, V.A. 2001. EVA: Large-scale analysis of secondary structure prediction. Proteins (Suppl) 5: 192-199.
    • (2001) Proteins (Suppl) , vol.5 , pp. 192-199
    • Rost, B.1    Eyrich, V.A.2
  • 26
    • 3342936478 scopus 로고    scopus 로고
    • A comprehensive analysis of 40 blind protein structure predictions
    • Samudrala, R. and Levitt, M. 2002. A comprehensive analysis of 40 blind protein structure predictions. BMC Struct. Biol. 2: 3-18.
    • (2002) BMC Struct. Biol. , vol.2 , pp. 3-18
    • Samudrala, R.1    Levitt, M.2
  • 27
    • 0032606133 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using a combined hierarchical approach
    • Samudrala, R., Xia, Y., Huang, E., and Levitt, M. 1999. Ab initio protein structure prediction using a combined hierarchical approach. Proteins (Suppl) 3: 194-198.
    • (1999) Proteins (Suppl) , vol.3 , pp. 194-198
    • Samudrala, R.1    Xia, Y.2    Huang, E.3    Levitt, M.4
  • 28
    • 0026223896 scopus 로고
    • A relational database for sequence-specific protein NMR data
    • Seavey, B.R., Farr, E.A., Westler, W.M., and Markley, J.L. 1991. A relational database for sequence-specific protein NMR data. J. Biomol. NMR 1: 217-236.
    • (1991) J. Biomol. NMR , vol.1 , pp. 217-236
    • Seavey, B.R.1    Farr, E.A.2    Westler, W.M.3    Markley, J.L.4
  • 29
    • 0347610773 scopus 로고
    • Empirical correlation between protein backbone conformation and Cα and Cβ NMR chemical shifts
    • Spera, S. and Bax, A. 1991. Empirical correlation between protein backbone conformation and Cα and Cβ NMR chemical shifts. J. Am. Chem. Soc. 113: 5490-5492.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 5490-5492
    • Spera, S.1    Bax, A.2
  • 31
    • 0026410969 scopus 로고
    • Relationship between nuclear magnetic resonance chemical shift and protein secondary structure
    • Wishart, D.S., Sykes, B.D., and Richards, F.M. 1991. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 222: 311-333.
    • (1991) J. Mol. Biol. , vol.222 , pp. 311-333
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 32
    • 0026597879 scopus 로고
    • The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy
    • -. 1992. The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31: 1647-1651.
    • (1992) Biochemistry , vol.31 , pp. 1647-1651


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