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.

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

• Python (with Tkinter)

• VTK (for graphics) including vtk-python -- see FAQ for the installation

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)

  • EM Data Bank

  • Wikipedia Software tools for Electron Microscopy (including UROX)