메뉴 건너뛰기




Volumn 10, Issue SUPPL. 1, 2009, Pages

Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures

Author keywords

[No Author keywords available]

Indexed keywords

3-DIMENSIONAL STRUCTURES; ELECTRON CRYO MICROSCOPIES; NATIVE STRUCTURES; PROTEIN COMPLEXES; PROTEIN SEQUENCES; SECONDARY STRUCTURE ELEMENTS; SECONDARY STRUCTURES; TOPOLOGICAL SPACES;

EID: 60849119541     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S40     Document Type: Article
Times cited : (5)

References (30)
  • 1
    • 0022539461 scopus 로고
    • Electron microscopy of frozen, hydrated biological specimens
    • 3087377
    • Chiu W Electron microscopy of frozen, hydrated biological specimens Annu Rev Biophys Biophys Chem 1986, 15:237-57 3087377
    • (1986) Annu Rev Biophys Biophys Chem , vol.15 , pp. 237-257
    • Chiu, W.1
  • 2
    • 0027264030 scopus 로고
    • What does electron cryomicroscopy provide that X-ray crystallography and NMR spectroscopy cannot?
    • 8347990
    • Chiu W What does electron cryomicroscopy provide that X-ray crystallography and NMR spectroscopy cannot? Annu Rev Biophys Biomol Struct 1993, 22:233-55 8347990
    • (1993) Annu Rev Biophys Biomol Struct , vol.22 , pp. 233-255
    • Chiu, W.1
  • 3
    • 0027214794 scopus 로고
    • Teaching electron diffraction and imaging of macromolecules
    • 1262489 8324196
    • Chiu W Schmid MF Prasad BV Teaching electron diffraction and imaging of macromolecules Biophys J 1993, 64:1610-25 1262489 8324196
    • (1993) Biophys J , vol.64 , pp. 1610-1625
    • Chiu, W.1    Schmid, M.F.2    Prasad, B.V.3
  • 4
    • 1842409555 scopus 로고    scopus 로고
    • Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy
    • 9052786
    • Bottcher B Wynne SA Crowther RA Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy Nature 1997, 386:88-91 9052786
    • (1997) Nature , vol.386 , pp. 88-91
    • Bottcher, B.1    Wynne, S.A.2    Crowther, R.A.3
  • 5
    • 0030888403 scopus 로고    scopus 로고
    • Pushing back the limits of electron cryomicroscopy
    • 9145097
    • Chiu W Schmid MF Pushing back the limits of electron cryomicroscopy Nat Struct Biol 1997, 4:331-3 9145097
    • (1997) Nat Struct Biol , vol.4 , pp. 331-333
    • Chiu, W.1    Schmid, M.F.2
  • 6
    • 0030937751 scopus 로고    scopus 로고
    • Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy
    • 9052787
    • Conway JF Cheng N Zlotnick A Wingfield PT Stahl SJ Steven AC Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy Nature 1997, 386:91-4 9052787
    • (1997) Nature , vol.386 , pp. 91-94
    • Conway, J.F.1    Cheng, N.2    Zlotnick, A.3    Wingfield, P.T.4    Stahl, S.J.5    Steven, A.C.6
  • 7
    • 0033854594 scopus 로고    scopus 로고
    • Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus
    • 10882067
    • Mancini EJ Clarke M Gowen BE Rutten T Fuller SD Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus Mol Cell 2000, 5:255-66 10882067
    • (2000) Mol Cell , vol.5 , pp. 255-266
    • Mancini, E.J.1    Clarke, M.2    Gowen, B.E.3    Rutten, T.4    Fuller, S.D.5
  • 10
    • 0036535896 scopus 로고    scopus 로고
    • Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches
    • 11959506
    • Chiu W Baker ML Jiang W Zhou ZH Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches Curr Opin Struct Biol 2002, 12:263-9 11959506
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 263-269
    • Chiu, W.1    Baker, M.L.2    Jiang, W.3    Zhou, Z.H.4
  • 11
    • 0037044862 scopus 로고    scopus 로고
    • Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography
    • 12424373
    • Medalia O Weber I Frangakis AS Nicastro D Gerisch G Baumeister W Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography Science 2002, 298:1209-13 12424373
    • (2002) Science , vol.298 , pp. 1209-1213
    • Medalia, O.1    Weber, I.2    Frangakis, A.S.3    Nicastro, D.4    Gerisch, G.5    Baumeister, W.6
  • 12
    • 0035906702 scopus 로고    scopus 로고
    • Bridging the information gap: Computational tools for intermediate resolution structure interpretation
    • 11352589
    • Jiang W Baker ML Ludtke SJ Chiu W Bridging the information gap: computational tools for intermediate resolution structure interpretation J Mol Biol 2001, 308:1033-44 11352589
    • (2001) J Mol Biol , vol.308 , pp. 1033-1044
    • Jiang, W.1    Baker, M.L.2    Ludtke, S.J.3    Chiu, W.4
  • 14
    • 0041507094 scopus 로고    scopus 로고
    • A structural-informatics approach for mining beta-sheets: Locating sheets in intermediate-resolution density maps
    • 12948490
    • Kong Y Ma J A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps J Mol Biol 2003, 332:399-413 12948490
    • (2003) J Mol Biol , vol.332 , pp. 399-413
    • Kong, Y.1    Ma, J.2
  • 15
    • 2342538953 scopus 로고    scopus 로고
    • A Structural-informatics approach for tracing beta-sheets: Building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps
    • 15123425
    • Kong Y Zhang X Baker TS Ma J A Structural-informatics approach for tracing beta-sheets: Building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps J Mol Biol 2004, 339:117-30 15123425
    • (2004) J Mol Biol , vol.339 , pp. 117-130
    • Kong, Y.1    Zhang, X.2    Baker, T.S.3    Ma, J.4
  • 16
    • 33846061281 scopus 로고    scopus 로고
    • Identification of secondary structure elements in intermediate-resolution density maps
    • 1810566 17223528
    • Baker ML Ju T Chiu W Identification of secondary structure elements in intermediate-resolution density maps Structure 2007, 15:7-19 1810566 17223528
    • (2007) Structure , vol.15 , pp. 7-19
    • Baker, M.L.1    Ju, T.2    Chiu, W.3
  • 17
    • 33750402176 scopus 로고    scopus 로고
    • A new representation for protein secondary structure prediction based on frequent patterns
    • 16940325
    • Birzele F Kramer S A new representation for protein secondary structure prediction based on frequent patterns Bioinformatics 2006, 22:2628-34 16940325
    • (2006) Bioinformatics , vol.22 , pp. 2628-2634
    • Birzele, F.1    Kramer, S.2
  • 18
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • 11933069
    • 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, 47:228-35 11933069
    • (2002) Proteins , vol.47 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 19
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • 10869041
    • McGuffin LJ Bryson K Jones DT The PSIPRED protein structure prediction server Bioinformatics 2000, 16:404-5 10869041
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 20
    • 20444490870 scopus 로고    scopus 로고
    • Determining protein topology from skeletons of secondary structures
    • 15961102
    • Wu Y Chen M Lu M Wang Q Ma J Determining protein topology from skeletons of secondary structures J Mol Biol 2005, 350:571-86 15961102
    • (2005) J Mol Biol , vol.350 , pp. 571-586
    • Wu, Y.1    Chen, M.2    Lu, M.3    Wang, Q.4    Ma, J.5
  • 21
    • 84863017077 scopus 로고    scopus 로고
    • Deriving Topology and Sequence Alignment for the Helix Skeleton in Low Resolution Protein Density Maps
    • Y Lu J He CEM Strauss Deriving Topology and Sequence Alignment for the Helix Skeleton in Low Resolution Protein Density Maps Proceeding of Asia-Pacific Bioinformatics Conference 2007, 143-52
    • (2007) Proceeding of Asia-Pacific Bioinformatics Conference , pp. 143-152
    • Lu, Y.1    He, J.2    Strauss, C.E.M.3
  • 22
    • 44049103480 scopus 로고    scopus 로고
    • Deriving topology and sequence alignment for the helix skeleton in low-resolution protein density maps
    • 18324752
    • Lu Y He J Strauss CE Deriving topology and sequence alignment for the helix skeleton in low-resolution protein density maps J Bioinform Comput Biol 2008, 6:183-201 18324752
    • (2008) J Bioinform Comput Biol , vol.6 , pp. 183-201
    • Lu, Y.1    He, J.2    Strauss, C.E.3
  • 23
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • 27033 10984534
    • Kuhlman B Baker D Native protein sequences are close to optimal for their structures Proc Natl Acad Sci USA 2000, 97:10383-8 27033 10984534
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 24
    • 0021819411 scopus 로고
    • A thermodynamical approach to the travelling salesman problem: An efficient simulation algorithm
    • Cerny V A thermodynamical approach to the travelling salesman problem: an efficient simulation algorithm Journal of Optimization Theory and Applications 1985, 45:41-51
    • (1985) Journal of Optimization Theory and Applications , vol.45 , pp. 41-51
    • Cerny, V.1
  • 26
    • 0037452727 scopus 로고    scopus 로고
    • Packing helices in proteins by global optimization of a potential energy function
    • 149897 12571353
    • Nanias M Chinchio M Pillardy J Ripoll DR Scheraga HA Packing helices in proteins by global optimization of a potential energy function Proc Natl Acad Sci USA 2003, 100:1706-10 149897 12571353
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 1706-1710
    • Nanias, M.1    Chinchio, M.2    Pillardy, J.3    Ripoll, D.R.4    Scheraga, H.A.5
  • 27
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S Jernigan RL Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation Macromolecules 1985, 18:534-552
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 28
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • 8604144
    • Miyazawa S Jernigan RL Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading J Mol Biol 1996, 256:623-44 8604144
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 29
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • 10493868
    • Jones DT Protein secondary structure prediction based on position-specific scoring matrices J Mol Biol 1999, 292:195-202 10493868
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.