메뉴 건너뛰기




Volumn 76, Issue 2, 2009, Pages 418-438

Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method

Author keywords

Automated protein structure analysis; Curvature; Secondary structure; Torsion

Indexed keywords

FERREDOXIN; STRUCTURAL PROTEIN;

EID: 67650233746     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22357     Document Type: Article
Times cited : (8)

References (36)
  • 1
    • 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
  • 2
    • 0026489233 scopus 로고
    • Anatomy and evolution of proteins displaying the viral capsid jellyroll topology
    • Chelvanayagam G, Heringa J, Argos P. Anatomy and evolution of proteins displaying the viral capsid jellyroll topology. J Mol Biol 1992;228:220-242.
    • (1992) J Mol Biol , vol.228 , pp. 220-242
    • Chelvanayagam, G.1    Heringa, J.2    Argos, P.3
  • 3
    • 0026773958 scopus 로고
    • Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features
    • Scheerlinck JPY, Lasters I, Claessem M, DeMaeyer M, Pio F, Delhause P, Wodak SJ. Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features. Proteins 1992;12:299-313.
    • (1992) Proteins , vol.12 , pp. 299-313
    • Scheerlinck, J.P.Y.1    Lasters, I.2    Claessem, M.3    DeMaeyer, M.4    Pio, F.5    Delhause, P.6    Wodak, S.J.7
  • 4
    • 0024279564 scopus 로고
    • General architecture of the a-helical globule
    • Murzin AG, Finkelstein AV. General architecture of the a-helical globule. J Mol Biol 1988;204:749-769.
    • (1988) J Mol Biol , vol.204 , pp. 749-769
    • Murzin, A.G.1    Finkelstein, A.V.2
  • 5
    • 0017387723 scopus 로고
    • β-Sheet topology and the relatedness of proteins
    • Richardson JS. β-Sheet topology and the relatedness of proteins. Nature 1977;268:495-500.
    • (1977) Nature , vol.268 , pp. 495-500
    • Richardson, J.S.1
  • 8
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, 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
  • 9
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1985;23:566-579.
    • (1985) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 10
    • 0020997912 scopus 로고
    • Dictionary of secondary structure of proteins: Pattern recognition of hydrogen-bonded and geometrical features
    • Sanger K. Dictionary of secondary structure of proteins: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Sanger, K.1
  • 11
    • 0023927904 scopus 로고
    • Identification of structural motifs from protien coordinate data: Secondary and first level supersecondary structure
    • Richards FM, Kundrot CE. Identification of structural motifs from protien coordinate data: secondary and first level supersecondary structure. Proteins 1988;3:71-84.
    • (1988) Proteins , vol.3 , pp. 71-84
    • Richards, F.M.1    Kundrot, C.E.2
  • 12
    • 0017701604 scopus 로고
    • Automatic identification of secondary structure in globular proteins
    • Levitt M, Greer J. Automatic identification of secondary structure in globular proteins. J Mol Biol 1977;114:181-293.
    • (1977) J Mol Biol , vol.114 , pp. 181-293
    • Levitt, M.1    Greer, J.2
  • 13
    • 0014347799 scopus 로고
    • Stereochemical criteria for polypeptides and proteins: Conformation of a system of three linked peptide units
    • Venkatachalam C. Stereochemical criteria for polypeptides and proteins: conformation of a system of three linked peptide units. Biopolymers 1968;6:1425-1436.
    • (1968) Biopolymers , vol.6 , pp. 1425-1436
    • Venkatachalam, C.1
  • 17
    • 0004062756 scopus 로고
    • Molecular Conformations and Biological Interactions: The 3-10 and alpha-helical conformation in peptides
    • Benedetti E, Blasio BD, Pavone V, Pedone C, Santini A, Crisma M, Toniolo C. Molecular Conformations and Biological Interactions: The 3-10 and alpha-helical conformation in peptides. Ind Acad Sci 1991;3:497-502.
    • (1991) Ind Acad Sci , vol.3 , pp. 497-502
    • Benedetti, E.1    Blasio, B.D.2    Pavone, V.3    Pedone, C.4    Santini, A.5    Crisma, M.6    Toniolo, C.7
  • 18
    • 0024278714 scopus 로고
    • 3Helix geometry in proteins
    • Barlow DJ, Thornton JM. 3Helix geometry in proteins. J Mol Biol 1988;201:601-619.
    • (1988) J Mol Biol , vol.201 , pp. 601-619
    • Barlow, D.J.1    Thornton, J.M.2
  • 19
    • 0033994775 scopus 로고    scopus 로고
    • HELANAL: A program to characterize helix geometry in proteins
    • Kumar S, Bansal M, Velavan R. HELANAL: a program to characterize helix geometry in proteins. J Biomol Struct Dyn 2000;17:811-819.
    • (2000) J Biomol Struct Dyn , vol.17 , pp. 811-819
    • Kumar, S.1    Bansal, M.2    Velavan, R.3
  • 20
    • 1642534352 scopus 로고    scopus 로고
    • Structural and functional characterization of pi bulges and other short interhelical deformations
    • Cartailler JP, Luecke H. Structural and functional characterization of pi bulges and other short interhelical deformations. Structure 2004;12:133-144.
    • (2004) Structure , vol.12 , pp. 133-144
    • Cartailler, J.P.1    Luecke, H.2
  • 22
    • 0030471018 scopus 로고    scopus 로고
    • A vector projection method for predicting supersecondary motifs
    • Sun Z-R, Zhang C-T, Wu F-H, Peng L-W. A vector projection method for predicting supersecondary motifs. J Protein Chem 1996;15:721-729.
    • (1996) J Protein Chem , vol.15 , pp. 721-729
    • Sun, Z.-R.1    Zhang, C.-T.2    Wu, F.-H.3    Peng, L.-W.4
  • 23
    • 0006522191 scopus 로고
    • Large molecules through atomic spectacles
    • Taylor H. Large molecules through atomic spectacles. Proc Am Phyl Soc 1941;85:1-12.
    • (1941) Proc Am Phyl Soc , vol.85 , pp. 1-12
    • Taylor, H.1
  • 25
    • 0027066845 scopus 로고
    • Differences in amino acid distribution of 3[10]-helices and alpha-helices
    • Karpen ME, De-Aseth PL, Neet KE. Differences in amino acid distribution of 3[10]-helices and alpha-helices. Protein Sci 1992;1:1333-1342.
    • (1992) Protein Sci , vol.1 , pp. 1333-1342
    • Karpen, M.E.1    De-Aseth, P.L.2    Neet, K.E.3
  • 27
    • 67650260355 scopus 로고    scopus 로고
    • Occurance, conformational features, and amino acid propensities for the pi-helix
    • Fodje MN, Al-Karadaghi S. Occurance, conformational features, and amino acid propensities for the pi-helix. Protein Eng 2002;15:533-358.
    • (2002) Protein Eng , vol.15 , pp. 533-358
    • Fodje, M.N.1    Al-Karadaghi, S.2
  • 29
    • 0027428284 scopus 로고
    • Standard structures in proteins
    • Efimov AV. Standard structures in proteins. Prog Biophys Mol Biol 1993;60:201-239.
    • (1993) Prog Biophys Mol Biol , vol.60 , pp. 201-239
    • Efimov, A.V.1
  • 30
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 A resolution
    • Vijayakumar S, Bugg CE, Cook WJ. Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 1987;194:531-544.
    • (1987) J Mol Biol , vol.194 , pp. 531-544
    • Vijayakumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 31
    • 17844366082 scopus 로고    scopus 로고
    • Multiple folding mechanisms of protien ubiquitin
    • Zhang J, Quin M, Wang W. Multiple folding mechanisms of protien ubiquitin. Proteins 2005;59:565-579.
    • (2005) Proteins , vol.59 , pp. 565-579
    • Zhang, J.1    Quin, M.2    Wang, W.3
  • 32
    • 84870649266 scopus 로고    scopus 로고
    • December 2008
    • Protein Data Bank. www.rcsb.org/pdb, December 2008.
    • Protein Data Bank
  • 33
    • 0021779081 scopus 로고    scopus 로고
    • Rose GD, Gierasch LM, Smith JA. Turns in peptides and proteins. Adv Prot Chem 1985;37:1-109.
    • Rose GD, Gierasch LM, Smith JA. Turns in peptides and proteins. Adv Prot Chem 1985;37:1-109.
  • 34
    • 67650229602 scopus 로고    scopus 로고
    • Ranganathan S, Izotov D, Kraka E, Cremer D. Projecting three-dimensional protein structure into a one-dimensional character code utilizing the automated protein structure analysis method. arXiv: 0811.3258 [q-bio.QM].
    • Ranganathan S, Izotov D, Kraka E, Cremer D. Projecting three-dimensional protein structure into a one-dimensional character code utilizing the automated protein structure analysis method. arXiv: 0811.3258 [q-bio.QM].
  • 35
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L, Sander C. Mapping the protein universe. Science 1996;273:595-603.
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.