Literature DB >> 16929111

NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps.

Karsten Suhre1, Jorge Navaza, Yves Henri Sanejouand.   

Abstract

This paper describes a freely available software suite that allows the modelling of large conformational changes of high-resolution three-dimensional protein structures under the constraint of a low-resolution electron-density map. Typical applications are the interpretation of electron-microscopy data using atomic scale X-ray structural models. The software package provided should enable the interested user to perform flexible fitting on new cases without encountering major technical difficulties. The NORMA software suite including three fully executable reference cases and extensive user instructions are available at http://www.elnemo.org/NORMA/.

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Year:  2006        PMID: 16929111     DOI: 10.1107/S090744490602244X

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  55 in total

1.  Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell.

Authors:  Wenjun Zheng; Mustafa Tekpinar
Journal:  Biophys J       Date:  2011-12-20       Impact factor: 4.033

2.  Cryoelectron microscopy structures of rotavirus NSP2-NSP5 and NSP2-RNA complexes: implications for genome replication.

Authors:  Xiaofang Jiang; Hariharan Jayaram; Mukesh Kumar; Steven J Ludtke; Mary K Estes; B V Venkataram Prasad
Journal:  J Virol       Date:  2006-08-23       Impact factor: 5.103

3.  Four-alpha-helix bundle with designed anesthetic binding pockets. Part I: structural and dynamical analyses.

Authors:  Dejian Ma; Nicole R Brandon; Tanxing Cui; Vasyl Bondarenko; Christian Canlas; Jonas S Johansson; Pei Tang; Yan Xu
Journal:  Biophys J       Date:  2008-02-29       Impact factor: 4.033

4.  Protein structure fitting and refinement guided by cryo-EM density.

Authors:  Maya Topf; Keren Lasker; Ben Webb; Haim Wolfson; Wah Chiu; Andrej Sali
Journal:  Structure       Date:  2008-02       Impact factor: 5.006

5.  Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution.

Authors:  Gunnar F Schröder; Axel T Brunger; Michael Levitt
Journal:  Structure       Date:  2007-12       Impact factor: 5.006

6.  Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography.

Authors:  Leonardo G Trabuco; Elizabeth Villa; Eduard Schreiner; Christopher B Harrison; Klaus Schulten
Journal:  Methods       Date:  2009-05-04       Impact factor: 3.608

7.  Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.

Authors:  Aqeel Ahmed; Paul C Whitford; Karissa Y Sanbonmatsu; Florence Tama
Journal:  J Struct Biol       Date:  2011-10-13       Impact factor: 2.867

8.  Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.

Authors:  Jen Hsin; James Gumbart; Leonardo G Trabuco; Elizabeth Villa; Pu Qian; C Neil Hunter; Klaus Schulten
Journal:  Biophys J       Date:  2009-07-08       Impact factor: 4.033

9.  Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.

Authors:  Marek Orzechowski; Florence Tama
Journal:  Biophys J       Date:  2008-10-10       Impact factor: 4.033

10.  Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.

Authors:  Leonardo G Trabuco; Elizabeth Villa; Kakoli Mitra; Joachim Frank; Klaus Schulten
Journal:  Structure       Date:  2008-05       Impact factor: 5.006

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