Fast Fitting of Atomic Structures to Low-resolution Electron Density Maps by Surface Overlap Maximization, Journal of Molecular Biology, vol.338, issue.4, pp.783-793, 2004. ,
DOI : 10.1016/j.jmb.2004.02.066
Multi-resolution contour-based fitting of macromolecular structures, Journal of Molecular Biology, vol.317, issue.3, pp.375-384, 2002. ,
DOI : 10.1006/jmbi.2002.5438
Visual Proteomics, Methods in Enzymology, vol.483, pp.215-243, 2010. ,
DOI : 10.1016/S0076-6879(10)83011-3
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage, Bioinformatics, vol.23, issue.4, pp.427-433, 2007. ,
DOI : 10.1093/bioinformatics/btl625
gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy, BMC Structural Biology, vol.13, issue.1, 2013. ,
DOI : 10.1016/j.jsb.2006.05.009
URL : https://hal.archives-ouvertes.fr/hal-00955580
PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis, Journal of Structural Biology, vol.178, issue.2, pp.177-188, 2012. ,
DOI : 10.1016/j.jsb.2011.12.003
Bridging the information gap: computational tools for intermediate resolution structure interpretation, Journal of Molecular Biology, vol.308, issue.5, pp.1033-1044, 2001. ,
DOI : 10.1006/jmbi.2001.4633
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques., Proceedings of the National Academy of Sciences, vol.89, issue.6, pp.2195-2199, 1992. ,
DOI : 10.1073/pnas.89.6.2195
Fast rotational matching, Acta Crystallographica Section D Biological Crystallography, vol.58, issue.8, pp.1282-1286, 2002. ,
DOI : 10.1107/S0907444902009794
EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.1, pp.28-39, 2007. ,
DOI : 10.1109/TCBB.2007.1003
Inferential Optimization for Simultaneous Fitting of Multiple Components into a CryoEM Map of Their Assembly, Journal of Molecular Biology, vol.388, issue.1, pp.180-194, 2009. ,
DOI : 10.1016/j.jmb.2009.02.031
ATP-bound states of GroEL captured by cryo-electron microscopy, Cell, vol.107, issue.7, pp.869-879, 2001. ,
CUDA C best practices guide. http://docs.nvidia.com/cuda/ cuda-c-best-practices-guide/index ,
UCSF Chimera?A visualization system for exploratory research and analysis, Journal of Computational Chemistry, vol.373, issue.13, pp.1605-1612, 2004. ,
DOI : 10.1002/jcc.20084
Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in Cryo-EM density maps, Biopolymers, vol.28, issue.9, pp.742-760, 2012. ,
DOI : 10.1002/bip.22074
Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions, Journal of Structural Biology, vol.170, issue.3, pp.427-438, 2010. ,
DOI : 10.1016/j.jsb.2010.03.007
Numerical Recipes: The Art of Scientific Computing, 2007. ,
Protein docking using spherical polar Fourier correlations, Proteins: Structure, Function, and Genetics, vol.3, issue.2, pp.178-194, 2000. ,
DOI : 10.1002/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6
URL : https://hal.archives-ouvertes.fr/inria-00434273
Accelerating protein-protein docking correlations using a six-dimensional analytic FFT generating function, Bioinformatics, vol.24, issue.4, pp.810-823, 2008. ,
Ultra-fast FFT protein docking on graphics processors, Bioinformatics, vol.26, issue.19, pp.2398-2405, 2010. ,
DOI : 10.1093/bioinformatics/btq444
URL : https://hal.archives-ouvertes.fr/inria-00537988
The watershed transform: definitions, algorithms and parallelization strategies, Fundamenta Informaticae, vol.41, pp.187-228, 2000. ,
Docking structures of domains into maps from cryo-electron microscopy using local correlation, Acta Crystallographica Section D Biological Crystallography, vol.56, issue.10, pp.1332-1340, 2000. ,
DOI : 10.1107/S0907444900010908
Particle finding in electron micrographs using a fast local correlation algorithm, Ultramicroscopy, vol.94, issue.3-4, pp.3-4, 2003. ,
DOI : 10.1016/S0304-3991(02)00333-9
Fitting atomic models into electron-microscopy maps, Acta Crystallographica Section D Biological Crystallography, vol.56, issue.10, pp.1341-1349, 2000. ,
DOI : 10.1107/S0907444900009562
Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs, Journal of Structural Biology, vol.178, issue.2, pp.121-128, 2012. ,
DOI : 10.1016/j.jsb.2012.03.001
: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps, Acta Crystallographica Section D Biological Crystallography, vol.62, issue.9, pp.1098-1100, 2006. ,
DOI : 10.1107/S090744490602244X
An adaptive Expectation???Maximization algorithm with GPU implementation for electron cryomicroscopy, Journal of Structural Biology, vol.171, issue.3, pp.256-265, 2010. ,
DOI : 10.1016/j.jsb.2010.06.004
Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy, Journal of Structural Biology, vol.149, issue.2, pp.191-203, 2005. ,
DOI : 10.1016/j.jsb.2004.11.004
Scoring functions for cryoEM density fitting, Journal of Structural Biology, vol.174, issue.2, pp.333-343, 2011. ,
DOI : 10.1016/j.jsb.2011.01.012
Quantitative Fitting of Atomic Models into Observed Densities Derived by Electron Microscopy, Journal of Structural Biology, vol.125, issue.2-3, pp.2-3, 1999. ,
DOI : 10.1006/jsbi.1998.4074
Using Situs for the integration of multi-resolution structures, Biophysical Reviews, vol.24, issue.1, pp.21-27, 2010. ,
DOI : 10.1007/s12551-009-0026-3
The RecA hexamer is a structural homologue of ring helicases, Nature Structural Biology, vol.6, issue.2, pp.101-104, 1997. ,
DOI : 10.1107/S0021889891004399
Multi-resolution contour-based fitting of macromolecular structures, Journal of Molecular Biology, vol.317, issue.3, pp.375-384, 2002. ,
DOI : 10.1006/jmbi.2002.5438
A Two-Stage Cross Correlation Approach to Template Matching, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.6, issue.3, pp.374-378, 1984. ,
DOI : 10.1109/TPAMI.1984.4767532
The watershed transform: definitions, algorithms and parallelization strategies, Fundamenta Informaticae, vol.41, pp.187-228, 2000. ,
Particle finding in electron micrographs using a fast local correlation algorithm, Ultramicroscopy, vol.94, issue.3-4, pp.3-4, 2003. ,
DOI : 10.1016/S0304-3991(02)00333-9