- Course overview
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- What are volume data?
- What is volume matching?
- What biological questions can we answer with volume matching?
- Volume pre-processing
- Volume-matching methodologies
- Scoring functions of volume matching
- Volume matching software
- Volume matching use case
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- References
References
1. Lagerstedt I., Moore W.J., Patwardhan A., Sanz-Garcia E., Best C., Swedlow J.R. and Kleywegt G.J. “Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB” J. Struct. Biol. 184, 173-181 (2013)
2. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC and Ferrin TE. (2004) “UCSF Chimera – a visualization system for exploratory research and analysis” J. Comput. Chem. 25(13):1605-12
3. Kawabata T (2008) “Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model” Biophys J., 95(10): 4643–4658.
4. Farabella I et al. (2015). “Tempy: A python library for assessment of 3D electron microscopy density fits”, J. Appl. Cryst. 48, 1314-1323
5. Roseman, A. M. (2000) “Docking structures of domains into maps from cryo-electron microscopy using local correlation” Acta Cryst. D 56, 1332–1340
6. Vasishtan D., and Topf, M. (2011) “Scoring functions for cryoEM density fitting” J. Struct. Biol. 174, 333-343
7. Chacón P., Wriggers W. (2002) “Multi-resolution contour-based fitting of macromolecular structures” J. Mol. Bio. 317(3): 375-384
8. Wu X, Milne JL, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR. (2003) “A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy” J. Struct. Biol. 141(1):63-76
9. Shatsky M, Hall RJ, Brenner SE, Glaeser RM. “A method for the alignment of heterogeneous macromolecules from electron microscopy” (2009) J. Struct. Biol. 166(1):67-78
10. Ceulemans H, Russell RB. “Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization” (2004) J. Struct. Biol. 338(4):783-793
11. Knossow, D., Ronfard, R. & Horaud, R. (2008) “Human motion tracking with a kinematic parameterization of extremal contours” Int. J. Comput. Vis.79, 247–269