메뉴 건너뛰기




Volumn 170, Issue 3, 2010, Pages 513-521

An automated procedure for detecting protein folds from sub-nanometer resolution electron density

Author keywords

Comparative modeling; Cryo electron microscopy; Fold prediction

Indexed keywords

GLYCOPROTEIN; GLYCOPROTEIN GP 1; GLYCOPROTEIN GP 10; GLYCOPROTEIN GP 4; UNCLASSIFIED DRUG;

EID: 77952585637     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2009.12.014     Document Type: Article
Times cited : (8)

References (51)
  • 3
    • 0030272365 scopus 로고    scopus 로고
    • Low resolution meets high: towards a resolution continuum from cells to atoms
    • Baker T.S., Johnson J.E. Low resolution meets high: towards a resolution continuum from cells to atoms. Curr. Opin. Struct. Biol. 1996, 6:585-594.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 585-594
    • Baker, T.S.1    Johnson, J.E.2
  • 5
    • 17044373783 scopus 로고    scopus 로고
    • The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes
    • Bubeck D., Filman D.J., Cheng N., Steven A.C., Hogle J.M., Belnap D.M. The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes. J. Virol. 2005, 79:7745-7755.
    • (2005) J. Virol. , vol.79 , pp. 7745-7755
    • Bubeck, D.1    Filman, D.J.2    Cheng, N.3    Steven, A.C.4    Hogle, J.M.5    Belnap, D.M.6
  • 6
    • 1942521664 scopus 로고    scopus 로고
    • Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization
    • Ceulemans H., Russell R.B. Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. J. Mol. Biol. 2004, 338:783-793.
    • (2004) J. Mol. Biol. , vol.338 , pp. 783-793
    • Ceulemans, H.1    Russell, R.B.2
  • 8
    • 48449106792 scopus 로고    scopus 로고
    • The Jpred 3 secondary structure prediction server
    • Cole C., Barber J.D., Barton G.J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 2008, 36:W197-W201.
    • (2008) Nucleic Acids Res. , vol.36
    • Cole, C.1    Barber, J.D.2    Barton, G.J.3
  • 9
    • 0037018948 scopus 로고    scopus 로고
    • Crystal structure of the malic enzyme from Ascaris suum complexed with nicotinamide adenine dinucleotide at 2.3A resolution
    • Coleman D.E., Rao G.S., Goldsmith E.J., Cook P.F., Harris B.G. Crystal structure of the malic enzyme from Ascaris suum complexed with nicotinamide adenine dinucleotide at 2.3A resolution. Biochemistry 2002, 41:6928-6938.
    • (2002) Biochemistry , vol.41 , pp. 6928-6938
    • Coleman, D.E.1    Rao, G.S.2    Goldsmith, E.J.3    Cook, P.F.4    Harris, B.G.5
  • 10
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with rosetta
    • Das R., Baker D. Macromolecular modeling with rosetta. Annu. Rev. Biochem. 2008, 77:363-382.
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 12
    • 0029975088 scopus 로고    scopus 로고
    • SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields
    • Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 1996, 116:190-199.
    • (1996) J. Struct. Biol. , vol.116 , pp. 190-199
    • Frank, J.1    Radermacher, M.2    Penczek, P.3    Zhu, J.4    Li, Y.5    Ladjadj, M.6    Leith, A.7
  • 13
    • 0037324306 scopus 로고    scopus 로고
    • Improving the performance of DomainParser for structural domain partition using neural network
    • Guo J.T., Xu D., Kim D., Xu Y. Improving the performance of DomainParser for structural domain partition using neural network. Nucleic Acids Res. 2003, 31:944-952.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 944-952
    • Guo, J.T.1    Xu, D.2    Kim, D.3    Xu, Y.4
  • 14
    • 39149143625 scopus 로고    scopus 로고
    • A comparative study of the reported performance of ab initio protein structure prediction algorithms
    • Helles G. A comparative study of the reported performance of ab initio protein structure prediction algorithms. J. R. Soc. Interface 2008, 5:387-396.
    • (2008) J. R. Soc. Interface , vol.5 , pp. 387-396
    • Helles, G.1
  • 15
    • 0035783171 scopus 로고    scopus 로고
    • Bsoft: image and molecular processing in electron microscopy
    • Heymann J.B. Bsoft: image and molecular processing in electron microscopy. J. Struct. Biol. 2001, 133:156-169.
    • (2001) J. Struct. Biol. , vol.133 , pp. 156-169
    • Heymann, J.B.1
  • 16
    • 33746338567 scopus 로고    scopus 로고
    • Partitioning protein structures into domains: why is it so difficult?
    • Holland T.A., Veretnik S., Shindyalov I.N., Bourne P.E. Partitioning protein structures into domains: why is it so difficult? J. Mol. Biol. 2006, 361:562-590.
    • (2006) J. Mol. Biol. , vol.361 , pp. 562-590
    • Holland, T.A.1    Veretnik, S.2    Shindyalov, I.N.3    Bourne, P.E.4
  • 17
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • Holm L., Sander C. Parser for protein folding units. Proteins 1994, 19:256-268.
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 18
    • 0035906702 scopus 로고    scopus 로고
    • Bridging the information gap: computational tools for intermediate resolution structure interpretation
    • Jiang W., Baker M.L., Ludtke S.J., Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 2001, 308:1033-1044.
    • (2001) J. Mol. Biol. , vol.308 , pp. 1033-1044
    • Jiang, W.1    Baker, M.L.2    Ludtke, S.J.3    Chiu, W.4
  • 19
    • 39849102970 scopus 로고    scopus 로고
    • Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy
    • Jiang W., Baker M.L., Jakana J., Weigele P.R., King J., Chiu W. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 2008, 451:1130-1134.
    • (2008) Nature , vol.451 , pp. 1130-1134
    • Jiang, W.1    Baker, M.L.2    Jakana, J.3    Weigele, P.R.4    King, J.5    Chiu, W.6
  • 20
    • 30044450170 scopus 로고    scopus 로고
    • Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses
    • Khayat R., Tang L., Larson E.T., Lawrence C.M., Young M., Johnson J.E. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Proc. Natl. Acad. Sci. USA 2005, 102:18944-18949.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 18944-18949
    • Khayat, R.1    Tang, L.2    Larson, E.T.3    Lawrence, C.M.4    Young, M.5    Johnson, J.E.6
  • 21
    • 0041507094 scopus 로고    scopus 로고
    • A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps
    • 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.
    • (2003) J. Mol. Biol. , vol.332 , pp. 399-413
    • Kong, Y.1    Ma, J.2
  • 22
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel E., Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:2256-2268.
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 23
    • 50849118817 scopus 로고    scopus 로고
    • Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM
    • Lander G.C., Evilevitch A., Jeembaeva M., Potter C.S., Carragher B., Johnson J.E. Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM. Structure 2008, 16:1399-1406.
    • (2008) Structure , vol.16 , pp. 1399-1406
    • Lander, G.C.1    Evilevitch, A.2    Jeembaeva, M.3    Potter, C.S.4    Carragher, B.5    Johnson, J.E.6
  • 24
  • 27
    • 34548643898 scopus 로고    scopus 로고
    • Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm
    • Liu X., Jiang W., Jakana J., Chiu W. Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J. struct. biol. 2007, 160:11-27.
    • (2007) J. struct. biol. , vol.160 , pp. 11-27
    • Liu, X.1    Jiang, W.2    Jakana, J.3    Chiu, W.4
  • 28
    • 0033377664 scopus 로고    scopus 로고
    • EMAN: semiautomated software for high-resolution single-particle reconstructions
    • Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 1999, 128:82-97.
    • (1999) J. Struct. Biol. , vol.128 , pp. 82-97
    • Ludtke, S.J.1    Baldwin, P.R.2    Chiu, W.3
  • 30
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., Brenner S.E., 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
  • 36
    • 0002660809 scopus 로고
    • The detection of sub-units within the crystallographic asymmetric unit
    • Rossmann M.G., Blow D.M. The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallogr. 1962, 15:24-32.
    • (1962) Acta Crystallogr. , vol.15 , pp. 24-32
    • Rossmann, M.G.1    Blow, D.M.2
  • 37
    • 5044235587 scopus 로고    scopus 로고
    • Electron crystallography reveals the structure of metarhodopsin I
    • Ruprecht J.J., Mielke T., Vogel R., Villa C., Schertler G.F. Electron crystallography reveals the structure of metarhodopsin I. EMBO J. 2004, 23:3609-3620.
    • (2004) EMBO J. , vol.23 , pp. 3609-3620
    • Ruprecht, J.J.1    Mielke, T.2    Vogel, R.3    Villa, C.4    Schertler, G.F.5
  • 39
    • 0021329694 scopus 로고
    • Steps in the stabilization of newly packaged DNA during phage P22 morphogenesis
    • Strauss H., King J. Steps in the stabilization of newly packaged DNA during phage P22 morphogenesis. J. Mol. Biol. 1984, 172:523-543.
    • (1984) J. Mol. Biol. , vol.172 , pp. 523-543
    • Strauss, H.1    King, J.2
  • 40
    • 3242883858 scopus 로고    scopus 로고
    • On the potential of normal-mode analysis for solving difficult molecular-replacement problems
    • Suhre K., Sanejouand Y.H. On the potential of normal-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:796-799.
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 796-799
    • Suhre, K.1    Sanejouand, Y.H.2
  • 42
    • 42949089487 scopus 로고    scopus 로고
    • Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
    • Trabuco L.G., Villa E., Mitra K., Frank J., Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 2008, 16:673-683.
    • (2008) Structure , vol.16 , pp. 673-683
    • Trabuco, L.G.1    Villa, E.2    Mitra, K.3    Frank, J.4    Schulten, K.5
  • 43
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: an automated program for molecular replacement
    • Vagin A., Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 1997, 30:1022-1025.
    • (1997) J. Appl. Cryst. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 45
    • 0036424944 scopus 로고    scopus 로고
    • A novel three-dimensional variant of the watershed transform for segmentation of electron density maps
    • Volkmann N. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J. Struct. Biol. 2002, 138:123-129.
    • (2002) J. Struct. Biol. , vol.138 , pp. 123-129
    • Volkmann, N.1
  • 46
    • 0032780181 scopus 로고    scopus 로고
    • Situs: a package for docking crystal structures into low-resolution maps from electron microscopy
    • Wriggers W., Milligan R.A., McCammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 1999, 125:185-195.
    • (1999) J. Struct. Biol. , vol.125 , pp. 185-195
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 47
    • 33845338800 scopus 로고    scopus 로고
    • AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles
    • Yan X., Sinkovits R.S., Baker T.S. AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct. Biol. 2007, 157:73-82.
    • (2007) J. Struct. Biol. , vol.157 , pp. 73-82
    • Yan, X.1    Sinkovits, R.S.2    Baker, T.S.3
  • 49
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • Zhang Y., Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005, 33:2302-2309.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 51
    • 34247619229 scopus 로고    scopus 로고
    • DDOMAIN: dividing structures into domains using a normalized domain-domain interaction profile
    • Zhou H., Xue B., Zhou Y. DDOMAIN: dividing structures into domains using a normalized domain-domain interaction profile. Protein Sci. 2007, 16:947-955.
    • (2007) Protein Sci. , vol.16 , pp. 947-955
    • Zhou, H.1    Xue, B.2    Zhou, Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.