Cryo-EM models

The cryo-EM revolution is sweeping structural biology. With the advent of the direct electron detector, cryo-EM (cryogenic electron microscopy) resolution rivals that of X-ray crystallography. We are automating the process of producing atomistic models from 3-D cryo-EM reconstructions.

MDfit

MDfit is a method that helps automate the final step in cryo-EM: going from 3-D map to atomistic model.

Tutorial 1

Tutorial 2

Source Code

Publications

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Head Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites

Ratje, A.H, Loerke, J, Mikolajka, A, Brünner, M, Hildebrand, P.W, Starosta, A.L, Dönhöfer, A, Connell, S.R, Fucini, P, Mielke, T, Whitford, P.C, Onuchic, J.N, Yu, Y, Sanbonmatsu, K.Y, Hartmann, R.K, Penczek, P.A, Wilson, D.N, and Spahn, C.M.T. (2010) Head Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites. Nature 468 (7324), 713-716, published December 2, 2010. doi:10.1038/nature09547. View PDF »

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Excited States of Ribosome Translocation Revealed through Integrative Molecular Modeling

Whitford, P.C, Ahmed, A, Yu, Y, Hennelly, S.P, Tama, F, Spahn, C.M.T, Onuchic, J.N, and Sanbonmatsu, K.Y. (2011) Excited States of Ribosome Translocation Revealed through Integrative Molecular Modeling. Proceedings of the National Academy of Sciences 108 (47), 18943-18948, published November 11, 2011. doi:10.1073/pnas.1108363108. View PDF »

GET IN TOUCH

Sanbonmatsu Team
Los Alamos National Laboratory
Theoretical Biology and Biophysics Group
P.O. Box 1663, Los Alamos, NM 87545
Public Affairs Office: (505) 667-7000
kys@lanl.gov