UROX Software
Interactive fitting of atomic models into Electron Microscopy reconstructions (and beyond...)
Developers : Xavier Siebert and Jorge Navaza
Last Release : 2.0.2 (August 2008)
What's new ?
[2010] A new version of UROX, renamed VEDA, is available on this page (main developer: Gael Goret).
[November 2008] This page starts as an attempt to maintain up-to-date information for UROX users, even though it is not my main project anymore.
[September 2008] Support for Mac versions was stopped, by decision of JN. Sorry.
[Summer 2008] Version 2.* now contains Normal-modes fitting as well as Map/Map fitting (in addition to the 'classical' model/map fitting).
Feedback is welcome !
Overview
UROX is a software initially designed for interactive fitting of high-resolution models (e.g, obtained by X-Ray crystallography) into Electron Microscopy reconstructions. It can also be used to fit two maps together (e.g., in tomography), or to perform Normal-modes calculations.
Snapshots
Downloads (32-bits Linux Binaries -- for now...)
Previous ("Stable") Linux version : 1.1.4
Current ("Testing") Linux version : 2.0.2
Installation
tar -zxvf urobin_{version_number}.tgz
cd UROX
source installbin_{version_number}.[c]sh (for csh or for sh)
then type 'urox' and enjoy (watch this video for a quick outlook)
Requirements
Publications
X. Siebert and J. Navaza : "UROX 2.0 : An interactive tool for fitting atomic models into Electron Microscopy reconstructions" Acta Crys (2009) D65, 651-658
J. Navaza et al. : "On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation", Acta Cryst. (2002). D58, 1820-1825
Recent Publications using/citing UROX (incomplete list, please let me know if yours is not included !) :
R. M. Glaeser et al., Model building and validation, Single-particle Cryo-EM of Biological Macromolecules (2021)
Si, D. et al., Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM, ArXiV 2102.06125 (2021)
Alnabati, E., & Kihara, D. Advances in Structure Modeling Methods forCryo-Electron Microscopy Maps. Molecules, 25(1), 82. (2020)
T. Kawabata - Rigid-Body Fitting of Atomic Models on 3D Density Maps of Electron Microscopy, Integrative Structural Biology with Hybrid Methods (2018)
Hoffmann, A. et al. "A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting." Journal of Applied Crystallography 50.4 (2017): 1036-1047.
Kuzu, Guray, et al. "PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps." Acta Crystallographica Section D: Structural Biology 72.10 (2016): 1137-1148.
E. Kandiah et al. " Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA", Scientific Reports 6, (2016)
Y. Chabal et al. " Structural rearrangements in the phage head-to-tail interface during assembly and infection", PNAS (2015)
S. Reich et al. "Structural insight into cap-snatching and RNA synthesis by influenza polymerase", Nature (2014)
J.R. López-Blanco, P. Chacón, "Structural modeling from electron microscopy data", WIREs Comput Mol Sci (2014)
G. Derevyanko and S. Grudinin, "HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions", Acta Cryst. D 70, 2069-2084 (2014)
Pickl-Herk et al. "Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle" P.N.A.S. (2013)
José Ramón Lopéz-Blanco and Pablo Chacón "iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinatesJR Lopéz-Blanco", J. Struct. Biol. (2013)
Estrozi et al. "Location of the dsRNA-Dependent Polymerase, VP1, in Rotavirus Particles"Advances", J. Mol. Biol. Available online 22 October 2012.
Chang et al. " Reconstructing Virus Structures from Nanometer to Near-Atomic Resolutions with Cryo-Electron Microscopy and Tomography", Advances in Experimental Medicine and Biology, Volume 726, 49-90 (2012)
Elegheert et al., "Extracellular Complexes of the Hematopoietic Human and Mouse CSF-1 Receptor Are Driven by Common Assembly Principles", Structure 19(12) 1762-1772 (2011)
Aramayo R. et al., "Quaternary structure of the specific p53–DNA complex reveals the mechanism of p53 mutant dominance" Nucl. Acids Res. (2011)
O. Pilak et al " Chaperonins from an Antarctic archaeon are predominantly monomeric: crystal structure of an open state monomer", Environmental Microbiology (2011)
M L. Baker et al. Modeling protein structure at near atomic resolutions with Gorgo, J. Struct. Biol (2011)
W. Wriggers et al. Matching structural densities from different biophysical origins with gain and bias (2011), J. Struct. Biol. 173(3), 445-450
M. Beak et al. Exploring the spatial and temporal organization of a cell's proteome, J. Struct. Biol (2011), 173(3) :483 - 496
N. Voss et al. Software Tools for Molecular Microscopy: An Open-Text Wikibook, Methods in Enzymology (2010) 482:381-392
M L. Baker et al. Analyses of Subnanometer Resolution Cryo-EM Density Maps, Methods in Enzymology (2010) 483: 1-29
Libersou S. et al. Distinct structural rearrangements of the VSV glycoprotein drive membrane fusion,(2010) J Cell Biol 191:199-210.
Baker ML et al., Analyses of Subnanometer Resolution Cryo-EM Density Maps, Methods in Enzymology, Academic Press (2010) Volume 483, Cryo-EM, Part C: Analyses, Interpretation, and Case studies, Pages 1-29.
J-K Hyun, Mazdak Radjainia, Richard L. Kingston, Alok K. Mitra, Proton-driven Assembly of the Rous Sarcoma Virus Capsid Protein Results in the Formation of Icosahedral Particles J. Biol. Chem. (2010) 285: 15056-15064.
He Y, Olson R. Three-dimensional structure of the detergent-solubilized Vibrio cholerae cytolysin (VCC) heptamer by electron cryomicroscopy., J Struct Biol. (2010), 169(1):6-13.
Okorokov AL, Chaban YL, Bugreev DV, Hodgkinson J, Mazin AV, et al. Structure of the hDmc1-ssDNA Filament Reveals the Principles of Its Architecture. PLoS ONE ( 2010), 5(1)
Sciara G. et al. Structure of lactococcal phage p2 baseplate and its mechanism of activation, P.N.A.S. (2010) 107 (15) 6852-6857
Martin D, Duarte M, Lepault J, Poncet D. Sequestration of Free Tubulin Molecules by the Viral Protein NSP2 Induces Microtubule Depolymerization during Rotavirus Infection. J.Virol (2009)
S. Muench et al. Cryo-electron Microscopy of the Vacuolar ATPase Motor Reveals its Mechanical and Regulatory Complexity, J Mol Biol (2009), 386 (4), 989 - 999.
Yongning He and Rich Olson, Three-dimensional structure of the detergent-solubilized Vibrio cholerae cytolysin (VCC) heptamer by electron cryomicroscopy, Journal of Structural Biology (2009)
Lhuillier et al. "Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating", P.N.A.S. (2009) 106 (21), 8507-8512
Suman Lata, et al. "Helical Structures of ESCRT-III Are Disassembled by VPS4", Science 321, 1354 (2008)
Hui Li, et al., "A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells", Science 321, 1357 (2008);
Dong-Hua Chen et al. "Location and Flexibility of the Unique C-Terminal Tail of Aquifex aeolicus Co-Chaperonin Protein 10 as Derived by Cryo-Electron Microscopy and Biophysical Techniques", J. Mol. Bio. (2008); 381 (3), 707-717
Mazdak Radjainia, Yu Wang and Alok K. Mitra, Structural Polymorphism of Oligomeric Adiponectin Visualized by Electron Microscopy, Journal of Molecular Biology Volume 381, Issue 2, Pages 419-430 (2008)
Libersou S., Siebert X., Ouldali M., Estrozi L. F., Navaza J., Charpilienne A., Garnier P., Poncet D. and Lepault J. ``Geometry mismatches within the concentric layers of rotavirus particles: a potential regulatory switch of the rotavirus transcription activity'', J. Virol. (2008); 82(6):2844-52
Gutsche I, Vujičić-Žagar A, Siebert X, Servant P, Vannier F, Castaing B, Gallet B, Heulin T, de Groot A, Sommer S, Serre L.
Complex oligomeric structure of a truncated form of DdrA: A protein required for the extreme radiotolerance of Deinococcus., Biochim Biophys Acta. 2008 Apr (see also the commentary in Nanoprobes)
Medical-Imaging-Week : news on UROX
Links
NORMA (normal mode fitting)
Wikipedia Software tools for Electron Microscopy (including UROX)