Literature DB >> 12238594

Reweighted atomic densities to represent ensembles of NMR structures.

Charles D Schwieters1, G Marius Clore.   

Abstract

A reweighted atomic probability density is introduced as a means of representing ensembles of NMR structures in a simple, concise and informative manner. This density is shown to give a better visual representation of molecular structure information than an unweighted density, and should provide a useful interactive graphics tool during the course of iterative NMR structure refinement. The approach is illustrated using several examples.

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Year:  2002        PMID： 12238594     DOI： 10.1023/a:1019875223132

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN： 0925-2738            Impact factor:   2.835


  14 in total

1.  Chi(1) rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force.

Authors:  G Marius Clore; John Kuszewski
Journal:  J Am Chem Soc       Date:  2002-03-27       Impact factor: 15.419

2.  Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy.

Authors:  G M Clore; A M Gronenborn
Journal:  Science       Date:  1991-06-07       Impact factor: 47.728

3.  Improved methods for building protein models in electron density maps and the location of errors in these models.

Authors:  T A Jones; J Y Zou; S W Cowan; M Kjeldgaard
Journal:  Acta Crystallogr A       Date:  1991-03-01       Impact factor: 2.290

4.  Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature.

Authors:  J F Doreleijers; G Vriend; M L Raves; R Kaptein
Journal:  Proteins       Date:  1999-11-15

5.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

6.  Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations.

Authors:  M Nilges; G M Clore; A M Gronenborn
Journal:  FEBS Lett       Date:  1988-03-14       Impact factor: 4.124

7.  Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin.

Authors:  G M Clore; A T Brünger; M Karplus; A M Gronenborn
Journal:  J Mol Biol       Date:  1986-10-05       Impact factor: 5.469

Review 8.  Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy.

Authors:  G M Clore; A M Gronenborn
Journal:  Crit Rev Biochem Mol Biol       Date:  1989       Impact factor: 8.250

9.  Representing an ensemble of NMR-derived protein structures by a single structure.

Authors:  M J Sutcliffe
Journal:  Protein Sci       Date:  1993-06       Impact factor: 6.725

10.  Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM-domain structures: one binds BAF and the other binds DNA.

Authors:  M Cai; Y Huang; R Ghirlando; K L Wilson; R Craigie; G M Clore
Journal:  EMBO J       Date:  2001-08-15       Impact factor: 11.598
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  35 in total

1.  Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy.

Authors:  Vincenzo Venditti; Nicolas L Fawzi; G Marius Clore
Journal:  J Biomol NMR       Date:  2011-09-04       Impact factor: 2.835

2.  Alignment of chain-like molecules.

Authors:  Martti Louhivuori; Kai Fredriksson; Kimmo Pääkkönen; Perttu Permi; Arto Annila
Journal:  J Biomol NMR       Date:  2004-08       Impact factor: 2.835

3.  Structural insights into charge pair interactions in triple helical collagen-like proteins.

Authors:  Jorge A Fallas; Jinhui Dong; Yizhi J Tao; Jeffrey D Hartgerink
Journal:  J Biol Chem       Date:  2011-12-17       Impact factor: 5.157

4.  Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.

Authors:  Daniel Gottstein; Donata K Kirchner; Peter Güntert
Journal:  J Biomol NMR       Date:  2012-02-22       Impact factor: 2.835

5.  NMR-based conformational ensembles explain pH-gated opening and closing of OmpG channel.

Authors:  Tiandi Zhuang; Christina Chisholm; Min Chen; Lukas K Tamm
Journal:  J Am Chem Soc       Date:  2013-10-01       Impact factor: 15.419

6.  Solution structure of the IIAChitobiose-HPr complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.

Authors:  Young-Sang Jung; Mengli Cai; G Marius Clore
Journal:  J Biol Chem       Date:  2012-05-16       Impact factor: 5.157

7.  Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy.

Authors:  Alexander N Volkov; Marcellus Ubbink; Nico A J van Nuland
Journal:  J Biomol NMR       Date:  2010-11-04       Impact factor: 2.835

8.  Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.

Authors:  Young-Sang Jung; Mengli Cai; G Marius Clore
Journal:  J Biol Chem       Date:  2009-12-03       Impact factor: 5.157

Review 9.  Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation.

Authors:  G Marius Clore
Journal:  Protein Sci       Date:  2011-02       Impact factor: 6.725

10.  pH-triggered, activated-state conformations of the influenza hemagglutinin fusion peptide revealed by NMR.

Authors:  Justin L Lorieau; John M Louis; Charles D Schwieters; Adriaan Bax
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-19       Impact factor: 11.205
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