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Volumn 196, Issue 3, 2016, Pages 289-298

De Novo modeling in cryo-EM density maps with Pathwalking

Author keywords

Backbone model; Protein structure

Indexed keywords

ARTICLE; BETA SHEET; CHEMICAL STRUCTURE; CLINICAL PROTOCOL; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; HUMAN; MACROMOLECULE; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY; ALGORITHM; MOLECULAR MODEL; PROCEDURES; PROTEIN CONFORMATION; SOFTWARE; ULTRASTRUCTURE;

EID: 84997208297     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2016.06.004     Document Type: Article
Times cited : (60)

References (53)
  • 2
    • 84924259507 scopus 로고    scopus 로고
    • The Traveling Salesman Problem: A Computational Study
    • Princeton University Press Princeton
    • Applegate, D.L., Bixby, R.E., Chvátal, V., Cook, W.J., The Traveling Salesman Problem: A Computational Study. 2006, Princeton University Press, Princeton.
    • (2006)
    • Applegate, D.L.1    Bixby, R.E.2    Chvátal, V.3    Cook, W.J.4
  • 3
    • 0041347832 scopus 로고    scopus 로고
    • Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics
    • Baker, Matthew L., Jiang, Wen, Bowman, Brian R., Hong Zhou, Z., Quiocho, Florante A., Rixon, Frazer J., Chiu, Wah, Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. J. Mol. Biol. 331:2 (2003), 447–456.
    • (2003) J. Mol. Biol. , vol.331 , Issue.2 , pp. 447-456
    • Baker, M.L.1    Jiang, W.2    Bowman, B.R.3    Hong Zhou, Z.4    Quiocho, F.A.5    Rixon, F.J.6    Chiu, W.7
  • 4
    • 33750976344 scopus 로고    scopus 로고
    • Automated segmentation of molecular subunits in electron cryomicroscopy density maps
    • Baker, Matthew L., Yu, Zeyun, Chiu, Wah, Bajaj, Chandrajit, Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J. Struct. Biol. 156:3 (2006), 432–441.
    • (2006) J. Struct. Biol. , vol.156 , Issue.3 , pp. 432-441
    • Baker, M.L.1    Yu, Z.2    Chiu, W.3    Bajaj, C.4
  • 5
    • 33846061281 scopus 로고    scopus 로고
    • Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps
    • Baker, Matthew L., Ju, Tao, Chiu, Wah, Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps. Structure 15:1 (2007), 7–19.
    • (2007) Structure , vol.15 , Issue.1 , pp. 7-19
    • Baker, M.L.1    Ju, T.2    Chiu, W.3
  • 6
    • 33846061281 scopus 로고    scopus 로고
    • Identification of secondary structure elements in intermediate-resolution density maps
    • Baker, Matthew L., Ju, Tao, Chiu, Wah, Identification of secondary structure elements in intermediate-resolution density maps. Structure 15:1 (2007), 7–19.
    • (2007) Structure , vol.15 , Issue.1 , pp. 7-19
    • Baker, M.L.1    Ju, T.2    Chiu, W.3
  • 7
    • 85001768357 scopus 로고    scopus 로고
    • Analyses of subnanometer resolution Cryo-EM density maps
    • vol. 483.
    • Baker, Matthew L., Baker, Mariah R., Hryc, Corey F., DiMaio, Frank., 2010. Analyses of subnanometer resolution Cryo-EM density maps, vol. 483.
    • (2010)
    • Baker Matthew, L.1    Baker Mariah, R.2    Hryc Corey, F.3    Frank, D.4
  • 8
  • 9
    • 77957585573 scopus 로고    scopus 로고
    • Cryo-EM of macromolecular assemblies at near-atomic resolution
    • Baker, Matthew L., Zhang, Junjie, Ludtke, Steven J., Chiu, Wah, Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat. Protoc. 5:10 (2010), 1697–1708.
    • (2010) Nat. Protoc. , vol.5 , Issue.10 , pp. 1697-1708
    • Baker, M.L.1    Zhang, J.2    Ludtke, S.J.3    Chiu, W.4
  • 10
    • 84862871445 scopus 로고    scopus 로고
    • Gorgon and pathwalking: Macromolecular modeling tools for subnanometer resolution density maps
    • In: Biopolymers, vol. 97, pp.
    • Baker, Matthew L., Baker, Mariah R., Hryc, Corey F., Ju, Tao., Chiu, Wah., 2012. Gorgon and pathwalking: Macromolecular modeling tools for subnanometer resolution density maps. In: Biopolymers, vol. 97, pp. 655–668.
    • (2012) , pp. 655-668
    • Baker Matthew, L.1    Baker Mariah, R.2    Hryc Corey, F.3    Tao, J.4    Wah, C.5
  • 11
    • 84857925824 scopus 로고    scopus 로고
    • Constructing and validating initial C?? models from subnanometer resolution density maps with pathwalking
    • Baker, Mariah R., Rees, Ian, Ludtke, Steven J., Chiu, Wah, Baker, Matthew L., Constructing and validating initial C?? models from subnanometer resolution density maps with pathwalking. Structure 20:3 (2012), 450–463.
    • (2012) Structure , vol.20 , Issue.3 , pp. 450-463
    • Baker, M.R.1    Rees, I.2    Ludtke, S.J.3    Chiu, W.4    Baker, M.L.5
  • 14
    • 84924617498 scopus 로고    scopus 로고
    • 2.8 Åresolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy
    • Campbell, Melody G., Veesler, David, Cheng, Anchi, Potter, Clinton S., Carragher, Bridget, 2.8 Åresolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. eLife, 4, 2015.
    • (2015) eLife , vol.4
    • Campbell, M.G.1    Veesler, D.2    Cheng, A.3    Potter, C.S.4    Carragher, B.5
  • 15
    • 84889594608 scopus 로고    scopus 로고
    • TRPV1 structures in distinct conformations reveal activation mechanisms
    • Cao, Erhu, Liao, Maofu, Cheng, Yifan, Julius, David, TRPV1 structures in distinct conformations reveal activation mechanisms. Nature 504:7478 (2013), 113–118.
    • (2013) Nature , vol.504 , Issue.7478 , pp. 113-118
    • Cao, E.1    Liao, M.2    Cheng, Y.3    Julius, D.4
  • 16
    • 84928400353 scopus 로고    scopus 로고
    • Single-particle cryo-EM at crystallographic resolution
    • Cheng, Yifan, Single-particle cryo-EM at crystallographic resolution. Cell 161:3 (2015), 450–457.
    • (2015) Cell , vol.161 , Issue.3 , pp. 450-457
    • Cheng, Y.1
  • 17
    • 85001835868 scopus 로고    scopus 로고
    • Electron cryomicroscopy of biological machines at subnanometer resolution
    • Chiu, Wah., Baker, Matthew L., Jiang, Wen., Dougherty, Matthew., Schmid, Michael F., 2005. Electron cryomicroscopy of biological machines at subnanometer resolution.
    • (2005)
    • Wah, C.1    Baker Matthew, L.2    Wen, J.3    Matthew, D.4    Schmid Michael, F.5
  • 18
    • 68949187842 scopus 로고    scopus 로고
    • Refinement of protein structures into low-resolution density maps using rosetta
    • DiMaio, Frank, Tyka, Michael D., Baker, Matthew L., Chiu, Wah, Baker, David, Refinement of protein structures into low-resolution density maps using rosetta. J. Mol. Biol. 392:1 (2009), 181–190.
    • (2009) J. Mol. Biol. , vol.392 , Issue.1 , pp. 181-190
    • DiMaio, F.1    Tyka, M.D.2    Baker, M.L.3    Chiu, W.4    Baker, D.5
  • 20
    • 84884812596 scopus 로고    scopus 로고
    • Computational methods for constructing protein structure models from 3D electron microscopy maps
    • Esquivel-Rodríguez, Juan, Kihara, Daisuke, Computational methods for constructing protein structure models from 3D electron microscopy maps. J. Struct. Biol. 184:1 (2013), 93–102.
    • (2013) J. Struct. Biol. , vol.184 , Issue.1 , pp. 93-102
    • Esquivel-Rodríguez, J.1    Kihara, D.2
  • 22
    • 84928560614 scopus 로고    scopus 로고
    • Structure of the E. coli ribosomeEF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM
    • Fischer, Niels, Neumann, Piotr, Konevega, Andrey L., Bock, Lars V., Ficner, Ralf, Rodnina, Marina V., Stark, Holger, Structure of the E. coli ribosomeEF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature, 2015.
    • (2015) Nature
    • Fischer, N.1    Neumann, P.2    Konevega, A.L.3    Bock, L.V.4    Ficner, R.5    Rodnina, M.V.6    Stark, H.7
  • 23
    • 84903700691 scopus 로고    scopus 로고
    • Protruding knob-like proteins violate local symmetries in an icosahedral marine virus
    • Gipson, Preeti, Baker, Matthew L, Raytcheva, Desislava, Haase-Pettingell, Cameron, Piret, Jacqueline, King, Jonathan a, Chiu, Wah, Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Nat. Commun., 5, 2014, 4278.
    • (2014) Nat. Commun. , vol.5 , pp. 4278
    • Gipson, P.1    Baker, M.L.2    Raytcheva, D.3    Haase-Pettingell, C.4    Piret, J.5    King, J.A.6    Chiu, W.7
  • 24
    • 77249150676 scopus 로고    scopus 로고
    • General k-opt submoves for the Lin–Kernighan TSP heuristic
    • Helsgaun, Keld, General k-opt submoves for the Lin–Kernighan TSP heuristic. Math. Program. Comput. 1:2-3 (2009), 119–163.
    • (2009) Math. Program. Comput. , vol.1 , Issue.2-3 , pp. 119-163
    • Helsgaun, K.1
  • 25
    • 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. 308:5 (2001), 1033–1044.
    • (2001) J. Mol. Biol. , vol.308 , Issue.5 , pp. 1033-1044
    • Jiang, W.1    Baker, M.L.2    Ludtke, S.J.3    Chiu, W.4
  • 26
    • 0037313264 scopus 로고    scopus 로고
    • Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions
    • Jiang, Wen, Li, Zongli, Zhang, Zhixian, Baker, Matthew L, Prevelige, Peter E, Chiu, Wah, Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat. Struct. Biol. 10:2 (2003), 131–135.
    • (2003) Nat. Struct. Biol. , vol.10 , Issue.2 , pp. 131-135
    • Jiang, W.1    Li, Z.2    Zhang, Z.3    Baker, M.L.4    Prevelige, P.E.5    Chiu, W.6
  • 27
    • 39849102970 scopus 로고    scopus 로고
    • Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy
    • Jiang, Wen, Baker, Matthew L., Jakana, Joanita, Weigele, Peter R., King, Jonathan, Chiu, Wah, Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 451:7182 (2008), 1130–1134.
    • (2008) Nature , vol.451 , Issue.7182 , pp. 1130-1134
    • Jiang, W.1    Baker, M.L.2    Jakana, J.3    Weigele, P.R.4    King, J.5    Chiu, W.6
  • 28
    • 84930637225 scopus 로고    scopus 로고
    • Atomic structure of anthrax protective antigen pore elucidates toxin translocation
    • Jiang, Jiansen, Pentelute, Bradley L., John Collier, R., Hong Zhou, Z., Atomic structure of anthrax protective antigen pore elucidates toxin translocation. Nature, 2015.
    • (2015) Nature
    • Jiang, J.1    Pentelute, B.L.2    John Collier, R.3    Hong Zhou, Z.4
  • 29
    • 84889607320 scopus 로고    scopus 로고
    • Structure of the TRPV1 ion channel determined by electron cryo-microscopy
    • Liao, Maofu, Cao, Erhu, Julius, David, Cheng, Yifan, Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:7478 (2013), 107–112.
    • (2013) Nature , vol.504 , Issue.7478 , pp. 107-112
    • Liao, M.1    Cao, E.2    Julius, D.3    Cheng, Y.4
  • 30
    • 84889607320 scopus 로고    scopus 로고
    • Structure of the TRPV1 ion channel determined by electron cryo-microscopy
    • Liao, Maofu, Cao, Erhu, Julius, David, Cheng, Yifan, Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:7478 (2013), 107–112.
    • (2013) Nature , vol.504 , Issue.7478 , pp. 107-112
    • Liao, M.1    Cao, E.2    Julius, D.3    Cheng, Y.4
  • 31
    • 84880848354 scopus 로고    scopus 로고
    • Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
    • Li, Xueming, Mooney, Paul, Zheng, Shawn, Booth, Christopher R., Braunfeld, Michael B., Gubbens, Sander, Agard, David A., Cheng, Yifan, Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10:6 (2013), 584–590.
    • (2013) Nat. Methods , vol.10 , Issue.6 , pp. 584-590
    • Li, X.1    Mooney, P.2    Zheng, S.3    Booth, C.R.4    Braunfeld, M.B.5    Gubbens, S.6    Agard, D.A.7    Cheng, Y.8
  • 33
    • 40049105503 scopus 로고    scopus 로고
    • De Novo backbone trace of GroEL from single particle electron cryomicroscopy
    • Ludtke, Steven J., Baker, Matthew L., Chen, Dong Hua, Song, Jiu Li, Chuang, David T., Chiu, Wah, De Novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16:3 (2008), 441–448.
    • (2008) Structure , vol.16 , Issue.3 , pp. 441-448
    • Ludtke, S.J.1    Baker, M.L.2    Chen, D.H.3    Song, J.L.4    Chuang, D.T.5    Chiu, W.6
  • 34
    • 40049105503 scopus 로고    scopus 로고
    • De Novo backbone trace of GroEL from single particle electron cryomicroscopy
    • Ludtke, Steven J., Baker, Matthew L., Chen, Dong Hua, Song, Jiu Li, Chuang, David T., Chiu, Wah, De Novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16:3 (2008), 441–448.
    • (2008) Structure , vol.16 , Issue.3 , pp. 441-448
    • Ludtke, S.J.1    Baker, M.L.2    Chen, D.H.3    Song, J.L.4    Chuang, D.T.5    Chiu, W.6
  • 38
    • 84862862508 scopus 로고    scopus 로고
    • Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in Cryo-EM density maps
    • In: Biopolymers, vol. 97, pp
    • Pintilie, Grigore., Chiu, Wah., 2012. Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in Cryo-EM density maps. In: Biopolymers, vol. 97, pp 742–760.
    • (2012) , pp. 742-760
    • Grigore, P.1    Wah, C.2
  • 40
    • 47749109511 scopus 로고    scopus 로고
    • Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel
    • Serysheva, Irina I., Ludtke, Steven J., Baker, Matthew L., Cong, Yao, Topf, Maya, Eramian, David, Sali, Andrej, Hamilton, Susan L., Chiu, Wah, Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc. Nat. Acad. Sci. U.S.A. 105:28 (2008), 9610–9615.
    • (2008) Proc. Nat. Acad. Sci. U.S.A. , vol.105 , Issue.28 , pp. 9610-9615
    • Serysheva, I.I.1    Ludtke, S.J.2    Baker, M.L.3    Cong, Y.4    Topf, M.5    Eramian, D.6    Sali, A.7    Hamilton, S.L.8    Chiu, W.9
  • 41
    • 33845332754 scopus 로고    scopus 로고
    • EMAN2: an extensible image processing suite for electron microscopy
    • Tang, Guang, Peng, Liwei, Baldwin, Philip R., Mann, Deepinder S., Jiang, Wen, Rees, Ian, Ludtke, Steven J., EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157:1 (2007), 38–46.
    • (2007) J. Struct. Biol. , vol.157 , Issue.1 , pp. 38-46
    • Tang, G.1    Peng, L.2    Baldwin, P.R.3    Mann, D.S.4    Jiang, W.5    Rees, I.6    Ludtke, S.J.7
  • 42
    • 12844256969 scopus 로고    scopus 로고
    • Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy
    • Topf, Maya, Baker, Matthew L., John, Bino, Chiu, Wah, Sali, Andrej, Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J. Struct. Biol. 149:2 (2005), 191–203.
    • (2005) J. Struct. Biol. , vol.149 , Issue.2 , pp. 191-203
    • Topf, M.1    Baker, M.L.2    John, B.3    Chiu, W.4    Sali, A.5
  • 43
    • 33645075435 scopus 로고    scopus 로고
    • Refinement of protein structures by iterative comparative modeling and cryoEM density fitting
    • Topf, Maya, Baker, Matthew L., Marti-Renom, Marc A., Chiu, Wah, Sali, Andrej, Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J. Mol. Biol. 357:5 (2006), 1655–1668.
    • (2006) J. Mol. Biol. , vol.357 , Issue.5 , pp. 1655-1668
    • Topf, M.1    Baker, M.L.2    Marti-Renom, M.A.3    Chiu, W.4    Sali, A.5
  • 44
    • 85001727380 scopus 로고    scopus 로고
    • Finding the right fit: chiseling structures out of cryo-electron microscopy maps
    • Villa, Elizabeth., Lasker, Keren., 2014. Finding the right fit: chiseling structures out of cryo-electron microscopy maps.
    • (2014)
    • Elizabeth, V.1    Keren, L.2
  • 46
    • 84904122902 scopus 로고    scopus 로고
    • Structure-based characterization of multiprotein complexes
    • Wiederstein, Markus, Gruber, Markus, Frank, Karl, Melo, Francisco, Sippl, Manfred J., Structure-based characterization of multiprotein complexes. Structure 22:7 (2014), 1063–1070.
    • (2014) Structure , vol.22 , Issue.7 , pp. 1063-1070
    • Wiederstein, M.1    Gruber, M.2    Frank, K.3    Melo, F.4    Sippl, M.J.5
  • 48
    • 43749092377 scopus 로고    scopus 로고
    • 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy
    • Yu, Xuekui, Jin, Lei, Zhou, Z Hong, 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Nature 453:7193 (2008), 415–419.
    • (2008) Nature , vol.453 , Issue.7193 , pp. 415-419
    • Yu, X.1    Jin, L.2    Zhou, Z.H.3
  • 51
    • 80052731717 scopus 로고    scopus 로고
    • 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus
    • Zhang, Rui, Hryc, Corey F., Cong, Yao, Liu, Xiangan, Jakana, Joanita, Gorchakov, Rodion, Baker, Matthew L., Weaver, Scott C., Chiu, Wah, 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. EMBO J. 30:18 (2011), 3854–3863.
    • (2011) EMBO J. , vol.30 , Issue.18 , pp. 3854-3863
    • Zhang, R.1    Hryc, C.F.2    Cong, Y.3    Liu, X.4    Jakana, J.5    Gorchakov, R.6    Baker, M.L.7    Weaver, S.C.8    Chiu, W.9
  • 52
    • 0034814786 scopus 로고    scopus 로고
    • Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus
    • Zhou, Z.H., Baker, M.L., Jiang, W., Dougherty, M., Jakana, J., Dong, G., Lu, G., Chiu, W., Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat. Struct. Biol. 8:10 (2001), 868–873.
    • (2001) Nat. Struct. Biol. , vol.8 , Issue.10 , pp. 868-873
    • Zhou, Z.H.1    Baker, M.L.2    Jiang, W.3    Dougherty, M.4    Jakana, J.5    Dong, G.6    Lu, G.7    Chiu, W.8
  • 53
    • 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, Jiang, Cheng, Lingpeng, Fang, Qin, Hong Zhou, Z., Honig, Barry, Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J. Mol. Biol. 397:3 (2010), 835–851.
    • (2010) J. Mol. Biol. , vol.397 , Issue.3 , pp. 835-851
    • Zhu, J.1    Cheng, L.2    Fang, Q.3    Hong Zhou, Z.4    Honig, B.5


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