Q: What paper should I cite if I use EMAN2 for a reconstruction ?
A: While we plan to publish something a bit more up to date documenting newer procedures in EMAN2, for now this the main reference to cite:
Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I. & Ludtke, S.J., 2007, EMAN2: an extensible image processing suite for electron microscopy, Journal of structural biology, 157(1), pp. 38-46.
There have been quite a few structures published with EMAN2 now, here are a few of the more impressive ones if you are looking for reliability information:
Park, E., Ménétret, J. F., Gumbart, J. C., Ludtke, S. J., Li, W., Whynot, A., Rapoport, T. A. & Akey, C. W. (2013) Structure of the SecY channel during initiation of protein translocation. Nature. PMID: 24153188
Chen, Z., Fischer, E. R., Kouiavskaia, D., Hansen, B. T., Ludtke, S. J., Bidzhieva, B., Makiya, M., Agulto, L., Purcell, R. H. & Chumakov, K. (2013) Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor. Proc. Natl. Acad. Sci. U. S. A. 110, 20242-20247.PMID: 24277851
Murray, S. C., Flanagan, J., Popova, O. B., Chiu, W., Ludtke, S. J. & Serysheva, I. I. (2013) Validation of Cryo-EM Structure of IP3R1 Channel. Structure. 21, 1-10. PMC3696195
Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW (2011) Structure of the Drosophila apoptosome at 6.9 å resolution. Structure 19: 128-140