메뉴 건너뛰기




Volumn 174, Issue 2, 2011, Pages 360-373

Modeling protein structure at near atomic resolutions with Gorgon

Author keywords

Cryo EM; Gorgon; Modeling; Near atomic resolution; Protein structure

Indexed keywords

ARTICLE; CRYOELECTRON MICROSCOPY; MATHEMATICAL ANALYSIS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE;

EID: 79954423522     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2011.01.015     Document Type: Article
Times cited : (81)

References (60)
  • 1
    • 78249251145 scopus 로고    scopus 로고
    • Semi-isometric registration of line features for flexible fitting of protein structures. Comput. Graph. Forum (Proceedings of Pacific Graphics 2010).
    • Abeysinghe, S., Baker, M.L., Chiu, W., Ju, T., 2010. Semi-isometric registration of line features for flexible fitting of protein structures. Comput. Graph. Forum (Proceedings of Pacific Graphics 2010).
    • (2010)
    • Abeysinghe, S.1    Baker, M.L.2    Chiu, W.3    Ju, T.4
  • 2
    • 48949116803 scopus 로고    scopus 로고
    • Shape modeling and matching in identifying 3D protein structures
    • Abeysinghe S., Ju T., Baker M.L., Chiu W. Shape modeling and matching in identifying 3D protein structures. Comput. Aided Des. 2008, 40:708-720.
    • (2008) Comput. Aided Des. , vol.40 , pp. 708-720
    • Abeysinghe, S.1    Ju, T.2    Baker, M.L.3    Chiu, W.4
  • 3
    • 50949105501 scopus 로고    scopus 로고
    • Segmentation-free skeletonization of grayscale volumes for shape understanding. In: IEEE International Conference on Shape Modeling and Applications
    • Abeysinghe, S.S., Baker, M.L., Chiu, W., Ju, T., 2008b. Segmentation-free skeletonization of grayscale volumes for shape understanding. In: IEEE International Conference on Shape Modeling and Applications, pp. 63-71.
    • (2008) , pp. 63-71
    • Abeysinghe, S.S.1    Baker, M.L.2    Chiu, W.3    Ju, T.4
  • 4
    • 67349259952 scopus 로고    scopus 로고
    • Interactive skeletonization of intensity volumes
    • Abeysinghe S.S., Ju T. Interactive skeletonization of intensity volumes. Vis. Comput. 2009, 25:627-635.
    • (2009) Vis. Comput. , vol.25 , pp. 627-635
    • Abeysinghe, S.S.1    Ju, T.2
  • 5
    • 77957282828 scopus 로고    scopus 로고
    • Analysis of subnanometer resolution cryo-EM density maps
    • Baker M.L., Baker M.R., Hryc C.F., Dimaio F. Analysis of subnanometer resolution cryo-EM density maps. Methods Enzymol. 2010, 483:1-29.
    • (2010) Methods Enzymol. , vol.483 , pp. 1-29
    • Baker, M.L.1    Baker, M.R.2    Hryc, C.F.3    Dimaio, F.4
  • 7
    • 33846061281 scopus 로고    scopus 로고
    • Identification of secondary structure elements in intermediate-resolution density maps
    • Baker M.L., Ju T., Chiu W. Identification of secondary structure elements in intermediate-resolution density maps. Structure 2007, 15:7-19.
    • (2007) Structure , vol.15 , pp. 7-19
    • Baker, M.L.1    Ju, T.2    Chiu, W.3
  • 9
    • 77957585573 scopus 로고    scopus 로고
    • Cryo-EM of macromolecular assemblies at near-atomic resolution
    • Baker M.L., Zhang J., Ludtke S.J., Chiu W. Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat. Protoc. 2010, 5:1697-1708.
    • (2010) Nat. Protoc. , vol.5 , pp. 1697-1708
    • Baker, M.L.1    Zhang, J.2    Ludtke, S.J.3    Chiu, W.4
  • 10
    • 79851508025 scopus 로고    scopus 로고
    • Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes
    • Birmanns S., Rusu M., Wriggers W. Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes. J StructBiol. 2010, 173:428-435.
    • (2010) J StructBiol. , vol.173 , pp. 428-435
    • Birmanns, S.1    Rusu, M.2    Wriggers, W.3
  • 11
    • 1842409555 scopus 로고    scopus 로고
    • Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy
    • Böttcher B., Wynne S.A., Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 1997, 386:88-91.
    • (1997) Nature , vol.386 , pp. 88-91
    • Böttcher, B.1    Wynne, S.A.2    Crowther, R.A.3
  • 15
    • 77649336015 scopus 로고    scopus 로고
    • Backbone model of an aquareovirusvirion by cryo-electron microscopy and bioinformatics
    • Cheng L., Zhu J., Hui W.H., Zhang X., Honig B., Fang Q., Zhou Z.H. Backbone model of an aquareovirusvirion by cryo-electron microscopy and bioinformatics. J. Mol. Biol. 2010, 397:852-863.
    • (2010) J. Mol. Biol. , vol.397 , pp. 852-863
    • Cheng, L.1    Zhu, J.2    Hui, W.H.3    Zhang, X.4    Honig, B.5    Fang, Q.6    Zhou, Z.H.7
  • 16
    • 14844325731 scopus 로고    scopus 로고
    • Electron cryomicroscopy of biological machines at subnanometer resolution
    • Chiu W., Baker M.L., Jiang W., Dougherty M., Schmid M.F. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 2005, 13:363-372.
    • (2005) Structure , vol.13 , pp. 363-372
    • Chiu, W.1    Baker, M.L.2    Jiang, W.3    Dougherty, M.4    Schmid, M.F.5
  • 17
    • 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. Nucl. Acids Res. 2008, 36:W197-W201.
    • (2008) Nucl. Acids Res. , vol.36
    • Cole, C.1    Barber, J.D.2    Barton, G.J.3
  • 19
    • 0030937751 scopus 로고    scopus 로고
    • Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy
    • Conway J.F., Cheng N., Zlotnick A., Wingfield P.T., Stahl S.J., Steven A.C. Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature 1997, 386:91-94.
    • (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
  • 20
    • 68949187842 scopus 로고    scopus 로고
    • Refinement of protein structures into low-resolution density maps using Rosetta
    • DiMaio F., Tyka M.D., Baker M.L., Chiu W., Baker D. Refinement of protein structures into low-resolution density maps using Rosetta. J. Mol. Biol. 2009, 392:181-190.
    • (2009) J. Mol. Biol. , vol.392 , pp. 181-190
    • DiMaio, F.1    Tyka, M.D.2    Baker, M.L.3    Chiu, W.4    Baker, D.5
  • 22
    • 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
  • 23
    • 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
  • 24
    • 0037313264 scopus 로고    scopus 로고
    • Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions
    • Jiang W., Li Z., Zhang Z., Baker M.L., Prevelige P.E., Chiu W. Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat. Struct. Biol. 2003, 10:131-135.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 131-135
    • Jiang, W.1    Li, Z.2    Zhang, Z.3    Baker, M.L.4    Prevelige, P.E.5    Chiu, W.6
  • 25
    • 0041561177 scopus 로고    scopus 로고
    • Semi-automated icosahedral particle reconstruction at sub-nanometer resolution
    • Jiang W., Li Z., Zhang Z., Booth C.R., Baker M.L., Chiu W. Semi-automated icosahedral particle reconstruction at sub-nanometer resolution. J. Struct. Biol. 2001, 136:214-225.
    • (2001) J. Struct. Biol. , vol.136 , pp. 214-225
    • Jiang, W.1    Li, Z.2    Zhang, Z.3    Booth, C.R.4    Baker, M.L.5    Chiu, W.6
  • 26
    • 34248218084 scopus 로고    scopus 로고
    • Computing a family of skeletons of volumetric models for shape description
    • Ju T., Baker M.L., Chiu W. Computing a family of skeletons of volumetric models for shape description. Comput. Aided Des. 2007, 39:352-360.
    • (2007) Comput. Aided Des. , vol.39 , pp. 352-360
    • Ju, T.1    Baker, M.L.2    Chiu, W.3
  • 27
    • 0030841589 scopus 로고    scopus 로고
    • Detecting folding motifs and similarities in protein structures
    • Kleywegt G.J., Jones T.A. Detecting folding motifs and similarities in protein structures. Methods Enzymol. 1997, 277:525-545.
    • (1997) Methods Enzymol. , vol.277 , pp. 525-545
    • Kleywegt, G.J.1    Jones, T.A.2
  • 28
    • 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
  • 29
    • 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
    • Kong Y., Zhang X., Baker T.S., 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, 339:117-130.
    • (2004) J. Mol. Biol. , vol.339 , pp. 117-130
    • Kong, Y.1    Zhang, X.2    Baker, T.S.3    Ma, J.4
  • 33
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin L.J., Bryson K., Jones D.T. The PSIPRED protein structure prediction server. Bioinformatics 2000, 16:404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 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
    • 14844338484 scopus 로고    scopus 로고
    • Combining X-ray crystallography and electron microscopy
    • Rossmann M.G., Morais M.C., Leiman P.G., Zhang W. Combining X-ray crystallography and electron microscopy. Structure 2005, 13:355-362.
    • (2005) Structure , vol.13 , pp. 355-362
    • Rossmann, M.G.1    Morais, M.C.2    Leiman, P.G.3    Zhang, W.4
  • 39
    • 0037435031 scopus 로고    scopus 로고
    • From words to literature in structural proteomics
    • Sali A., Glaeser R., Earnest T., Baumeister W. From words to literature in structural proteomics. Nature 2003, 422:216-225.
    • (2003) Nature , vol.422 , pp. 216-225
    • Sali, A.1    Glaeser, R.2    Earnest, T.3    Baumeister, W.4
  • 40
    • 0033400935 scopus 로고    scopus 로고
    • Challenges at the frontiers of structural biology
    • Sali A., Kuriyan J. Challenges at the frontiers of structural biology. Trends Cell Biol. 1999, 9:M20-M24.
    • (1999) Trends Cell Biol. , vol.9
    • Sali, A.1    Kuriyan, J.2
  • 42
    • 79954420150 scopus 로고    scopus 로고
    • Structure. In: NIH workshop on structural proteomics of biological complexes. United States (unknown reference type).
    • Sali, A., 2003. Structure. In: NIH workshop on structural proteomics of biological complexes. United States (unknown reference type).
    • (2003)
    • Sali, A.1
  • 43
    • 36749078686 scopus 로고    scopus 로고
    • Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution
    • Schröder G.F., Brunger A.T., Levitt M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 2007, 15:1630-1641.
    • (2007) Structure , vol.15 , pp. 1630-1641
    • Schröder, G.F.1    Brunger, A.T.2    Levitt, M.3
  • 45
    • 68149149564 scopus 로고    scopus 로고
    • UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions
    • Siebert X., Navaza J. UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions. Acta Crystallogr. D Biol. Crystallogr. 2009, 65:651-658.
    • (2009) Acta Crystallogr. D Biol. Crystallogr. , vol.65 , pp. 651-658
    • Siebert, X.1    Navaza, J.2
  • 46
    • 4344716056 scopus 로고    scopus 로고
    • Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
    • Tama F., Miyashita O., Brooks C.L. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 2004, 147:315-326.
    • (2004) J. Struct. Biol. , vol.147 , pp. 315-326
    • Tama, F.1    Miyashita, O.2    Brooks, C.L.3
  • 47
    • 12844256969 scopus 로고    scopus 로고
    • Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy
    • Topf M., Baker M.L., John B., Chiu W., Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J. Struct. Biol. 2005, 149:191-203.
    • (2005) J. Struct. Biol. , vol.149 , pp. 191-203
    • Topf, M.1    Baker, M.L.2    John, B.3    Chiu, W.4    Sali, A.5
  • 48
    • 33645075435 scopus 로고    scopus 로고
    • Refinement of protein structures by iterative comparative modeling and CryoEM density fitting
    • Topf M., Baker M.L., Marti-Renom M.A., Chiu W., Sali A. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J. Mol. Biol. 2006, 357:1655-1668.
    • (2006) J. Mol. Biol. , vol.357 , pp. 1655-1668
    • Topf, M.1    Baker, M.L.2    Marti-Renom, M.A.3    Chiu, W.4    Sali, A.5
  • 49
    • 38949092920 scopus 로고    scopus 로고
    • Protein structure fitting and refinement guided by cryo-EM density
    • Topf M., Lasker K., Webb B., Wolfson H., Chiu W., Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 2008, 16:295-307.
    • (2008) Structure , vol.16 , pp. 295-307
    • Topf, M.1    Lasker, K.2    Webb, B.3    Wolfson, H.4    Chiu, W.5    Sali, A.6
  • 50
    • 70349267547 scopus 로고    scopus 로고
    • Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography
    • Trabuco L.G., Villa E., Schreiner E., Harrison C.B., Schulten K. Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods 2009, 49:174-180.
    • (2009) Methods , vol.49 , pp. 174-180
    • Trabuco, L.G.1    Villa, E.2    Schreiner, E.3    Harrison, C.B.4    Schulten, K.5
  • 52
    • 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
  • 53
    • 43749092377 scopus 로고    scopus 로고
    • 3.88 A structure of cytoplasmicpolyhedrosis virus by cryo-electron microscopy
    • Yu X., Jin L., Zhou Z.H. 3.88 A structure of cytoplasmicpolyhedrosis virus by cryo-electron microscopy. Nature 2008, 453:415-419.
    • (2008) Nature , vol.453 , pp. 415-419
    • Yu, X.1    Jin, L.2    Zhou, Z.H.3
  • 55
    • 77951912692 scopus 로고    scopus 로고
    • 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry
    • Zhang X., Jin L., Fang Q., Hui W.H., Zhou Z.H. 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry. Cell 2010, 141:472-482.
    • (2010) Cell , vol.141 , pp. 472-482
    • Zhang, X.1    Jin, L.2    Fang, Q.3    Hui, W.H.4    Zhou, Z.H.5
  • 57
    • 41949099222 scopus 로고    scopus 로고
    • Towards atomic resolution structural determination by single-particle cryo-electron microscopy
    • Zhou Z.H. Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Curr. Opin. Struct. Biol. 2008, 18:218-228.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 218-228
    • Zhou, Z.H.1
  • 60
    • 77649336168 scopus 로고    scopus 로고
    • Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement
    • Zhu J., Cheng L., Fang Q., Zhou Z.H., Honig B. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J. Mol. Biol. 2010, 397:835-851.
    • (2010) J. Mol. Biol. , vol.397 , pp. 835-851
    • Zhu, J.1    Cheng, L.2    Fang, Q.3    Zhou, Z.H.4    Honig, B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.