Scoring functions for cryoEM density fitting

Journal of Structural Biology

Volumn 174, Issue 2, 2011, Pages 333-343

  Vasishtan, Daven ^a   Topf, Maya ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Cross correlation function; Density fitting; Electron cryo microscopy; Envelope score; Laplacian filtering; Mutual information; Scoring functions

Indexed keywords

ARTICLE; CRYOELECTRON MICROSCOPY; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE;

ALGORITHMS; CHAPERONIN 60; COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; MATHEMATICAL COMPUTING; MODELS, MOLECULAR; PROTEIN CONFORMATION; STATISTICS, NONPARAMETRIC; SURFACE PROPERTIES;

EID: 79954417945     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2011.01.012     Document Type: Article

References (27)

1. Beck, M., M. Topf, Z. Frazier, H. Tjong, M. Xu, S. Zhang, and F. Alber, (in press). Exploring the spatial and temporal organization of a cell's proteome. J. Struct. Biol.
2. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucl. Acids Res. 2000, 28:235-242.
3. Ceulemans H., Russell R.B. Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. J. Mol. Biol. 2004, 338:783-793.
4. Chacon P., Wriggers W. Multi-resolution contour-based fitting of macromolecular structures. J. Mol. Biol. 2002, 317:375-384.
5. Chen Z., Husz Z.L., Wallace I., Wallace A.M. Video object tracking based on a Chamfer distance transform. IEEE Int. Conf. Image Process. 2007, 3:357-360.
6. Chiu W., Baker M.L., Jiang W., Dougherty M., Schmid M.F. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure (Camb) 2005, 13:363-372.
7. Cover, T.M., Thomas, J.A. 2006. Elements of Information Theory, 2nd ed. Wiley Interscience.
8. Fabiola F., Chapman M.S. Fitting of high-resolution structures into electron microscopy reconstruction images. Structure (Camb) 2005, 13:389-400.
9. Frank J. Single-particle reconstruction of biological macromolecules in electron microscopy - 30 years. Q Rev. Biophysics. 2009, 42:139-158.
10. Harpaz Y., Gerstein M., Chothia C. Volume changes on protein folding. Structure 1994, 2:641-649.
11. Jones, E., Oliphant, T., et al. 2001. Scipy: open source scientific tools for Python, 2010.
12. Knossow D., Ronfard R., Horaud R. Human motion tracking with a kinematic parameterization of extremal contours. Int. J. Comput. Vision 2008, 79:247-269.
13. Lasker K., Topf M., Sali A., Wolfson H.J. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J. Mol. Biol. 2009, 388:180-194.
14. Lawson, C.L., Baker, M.L., Best, C., Bi, C., Dougherty, M., Feng, P., van Ginkel, G., Devkota, B., Lagerstedt, I., Ludtke, S.J., Newman, R.H., Oldfield, T.J., Rees, I., Sahni, G., Sala, R., Velankar, S., Warren, J., Westbrook, J.D., Henrick, K., Kleywegt, G.J., Berman, H.M., Chiu, W. (in press). EMDataBank.org: unified data resource for cryoEM. Nucleic Acids Res. 2011 Database Issue.
15. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
16. Roseman A.M. Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr. D Biol. Crystallogr. 2000, 56:1332-1340.
17. Rossmann M.G. Fitting atomic models into electron-microscopy maps. Acta Crystallogr. D Biol. Crystallogr. 2000, 56:1341-1349.
18. Rossmann M.G., Morais M.C., Leiman P.G., Zhang W. Combining X-ray crystallography and electron microscopy. Structure 2005, 13:355-362.
19. Saha M., Levitt M., Chiu W. MOTIF-EM: an automated computational tool for identifying conserved regions in cryoEM structures. Bioinformatics 2010, 26:301-309.
20. Shatsky M., Hall R.J., Brenner S.E., Glaeser R.M. A method for the alignment of heterogeneous macromolecules from electron microscopy. J. Struct. Biol. 2008, 166:67-78.
21. R Development Core Team, 2008. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org.
22. Tung C.-C., Lobo P.A., Kimlicka L., Van Petegem F. The amino-terminal disease hotspot of ryanodine receptors forms a cytoplasmic vestibule. Nature 2010, 468:585-588.
23. Team RDC: R: a language and environment for statistical computing. R Foundation for Statistical Computing 2008.
24. Volkmann N. Confidence intervals for fitting of atomic models into low-resolution densities. Acta Crystallogr. D Biol. Crystallogr. 2009, 65:679-689.
25. Wriggers W., Chacon P. Modeling tricks and fitting techniques for multiresolution structures. Structure (Camb) 2001, 9:779-788.
26. 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.
27. Wu X., Milne J.L., Borgnia M.J., Rostapshov A.V., Subramaniam S., Brooks B.R. A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J. Struct. Biol. 2003, 141:63-76.