High resolution single particle refinement in EMAN2.1

Methods

Volumn 100, Issue , 2016, Pages 25-34

  Bell, James M ^a   Chen, Muyuan ^a   Baldwin, Philip R ^a   Ludtke, Steven J ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

3 D reconstruction; CryoEM; Image processing; Single particle analysis; Structural biology

Indexed keywords

ARTICLE; CONTROLLED STUDY; EMAN2.1 SOFTWARE; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE QUALITY; IMAGE RECONSTRUCTION; IMAGING AND DISPLAY; IMAGING SOFTWARE; MONTE CARLO METHOD; PRIORITY JOURNAL; SIGNAL NOISE RATIO; THREE DIMENSIONAL IMAGING; TWO DIMENSIONAL IMAGING; VALIDATION PROCESS; ALGORITHM; CRYOELECTRON MICROSCOPY; MOLECULAR MODEL; PRINCIPAL COMPONENT ANALYSIS; SOFTWARE; TRANSMISSION ELECTRON MICROSCOPY;

ALGORITHMS; CRYOELECTRON MICROSCOPY; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, ELECTRON, TRANSMISSION; MODELS, MOLECULAR; PRINCIPAL COMPONENT ANALYSIS; SOFTWARE;

EID: 84959182065     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.02.018     Document Type: Article

References (33)

1. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. J. Struct. Biol. 1996, 116:190-199.
2. Frank J. Ultramicroscopy 1981, 6:343-357.
3. van Heel M., Harauz G., Orlova E.V., Schmidt R., Schatz M. J. Struct. Biol. 1996, 116:17-24.
4. Tang G., Peng L., Baldwin P.R., Mann D.S., Jiang W., Rees I., Ludtke S.J. J. Struct. Biol. 2007, 157:38-46.
5. Hohn M., Tang G., Goodyear G., Baldwin P.R., Huang Z., Penczek P.A., Yang C., Glaeser R.M., Adams P.D., Ludtke S.J. J. Struct. Biol. 2007, 157:47-55.
6. Scheres S.H. J. Struct. Biol. 2012, 180:519-530.
7. Scheres S.H.W., Núñez-Ramírez R., Sorzano C.O.S., Carazo J.M., Marabini R. Nat. Protoc. 2008, 3:977-990.
8. Grigorieff N. J. Struct. Biol. 2007, 157:117-125.
9. Dubochet J., Chang J.-J., Freeman R., Lepault J., McDowall A.W. Ultramicroscopy 1982, 10:55-61.
10. Erickson H.P., Klug A. Philos. Trans. R. Soc. Lond. B 1970, 261:221-230.
11. Jin L., Milazzo A.-C., Kleinfelder S., Li S., Leblanc P., Duttweiler F., Bouwer J.C., Peltier S.T., Ellisman M.H., Xuong N.-H. J. Struct. Biol. 2008, 161:352-358.
12. Campbell M.G., Cheng A., Brilot A.F., Moeller A., Lyumkis D., Veesler D., Pan J., Harrison S.C., Potter C.S., Carragher B., Grigorieff N. Structure 2012, 20:1823-1828.
13. Rubinstein J.L., Brubaker M.A. J. Struct. Biol. 2015, 192:188-195.
14. Bai X.C., Fernandez I.S., McMullan G., Scheres S.H. Elife 2013, 2:e00461.
15. Li X., Mooney P., Zheng S., Booth C.R., Braunfeld M.B., Gubbens S., Agard D.A., Cheng Y. Nat. Methods 2013, 10:584-590.
16. Wang Z., Hryc C.F., Bammes B., Afonine P.V., Jakana J., Chen D.H., Liu X., Baker M.L., Kao C., Ludtke S.J., Schmid M.F., Adams P.D., Chiu W. Nat. Commun. 2014, 5:4808.
17. Mindell J.A., Grigorieff N. J. Struct. Biol. 2003, 142:334-347.
18. Zhu Y., Carragher B., Glaeser R.M., Fellmann D., Bajaj C., Bern M., Mouche F., de Haas F., Hall R.J., Kriegman D.J., Ludtke S.J., Mallick S.P., Penczek P.A., Roseman A.M., Sigworth F.J., Volkmann N., Potter C.S. J. Struct. Biol. 2004, 145:3-14.
19. Woolford D., Ericksson G., Rothnagel R., Muller D., Landsberg M.J., Pantelic R.S., McDowall A., Pailthorpe B., Young P.R., Hankamer B., Banks J. J. Struct. Biol. 2007, 157:174-188.
20. Kivioja T., Ravantti J., Verkhovsky A., Ukkonen E., Bamford D. J. Struct. Biol. 2000, 131:126-134.
21. Ludtke S.J., Jakana J., Song J.L., Chuang D.T., Chiu W. J. Mol. Biol. 2001, 314:253-262.
22. Cong Y., Schröder G.F., Meyer A.S., Jakana J., Ma B., Dougherty M.T., Schmid M.F., Reissmann S., Levitt M., Ludtke S.L., Frydman J., Chiu W. EMBO J. 2012, 31:720-730.
23. Baldwin P.R., Penczek P.A. J. Struct. Biol. 2007, 157:250-261.
24. Van Heel M. Ultramicroscopy 1987, 21:111-123.
25. Elmlund H., Elmlund D., Bengio S. Structure 2013, 21:1299-1306.
26. Galaz-Montoya J.G., Flanagan J., Schmid M.F., Ludtke S.J. J. Struct. Biol. 2015, 190:279-290.
27. Bartesaghi A., Matthies D., Banerjee S., Merk A., Subramaniam S. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:11709-11714.
28. Schröder G.F. Curr. Opin. Struct. Biol. 2015, 31:20-27.
29. Baker M.L., Abeysinghe S.S., Schuh S., Coleman R.A., Abrams A., Marsh M.P., Hryc C.F., Ruths T., Chiu W., Ju T. J. Struct. Biol. 2011, 174:360-373.
30. Baker M., Rees I., Ludtke S., Chiu W., Baker M. Structure 2012, 20:450-463.
31. Henderson R., Sali A., Baker M.L., Carragher B., Devkota B., Downing K.H., Egelman E.H., Feng Z., Frank J., Grigorieff N., Jiang W., Ludtke S.J., Medalia O., Penczek P.A., Rosenthal P.B., Rossmann M.G., Schmid M.F., Schröder G.F., Steven A.C., Stokes D.L., Westbrook J.D., Wriggers W., Yang H., Young J., Berman H.M., Chiu W., Kleywegt G.J., Lawson C.L. Structure 2012, 20:205-214.
32. Chen V.B., Arendall W.B., Headd J.J., Keedy D.A., Immormino R.M., Kapral G.J., Murray L.W., Richardson J.S., Richardson D.C. Acta Crystallogr. D Biol. Crystallogr. 2010, 66:12-21.
33. Murray S.C., Flanagan J., Popova O.B., Chiu W., Ludtke S.J., Serysheva I.I. Structure 2013, 21:900-909.