NMRFAM-SPARKY: Enhanced software for biomolecular NMR spectroscopy

Bioinformatics

Volumn 31, Issue 8, 2015, Pages 1325-1327

  Lee, Woonghee ^a   Tonelli, Marco ^a   Markley, John L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

CHEMISTRY; COMPUTER PROGRAM; HUMAN; NUCLEAR MAGNETIC RESONANCE; PROCEDURES; PROTEIN DATABASE;

DATABASES, PROTEIN; HUMANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; SOFTWARE;

EID: 84927748573     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu830     Document Type: Article

References (17)

1. Bahrami, A. et al. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol, 5, e1000307.
2. Bartels, C. et al. (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR, 6, 1-10.
3. Berman, H. et al. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
4. Chen, V. B. et al. (2010)MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr., 66, 12-21.
5. Eghbalnia, H. R. et al. (2005) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J. Biomol. NMR, 32, 71-81.
6. Frishman, D. and Argos, P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579.
7. Goddard, T. D. and Kneller, D. G. (2008) SPARKY 3.University of California, San Francisco, CA.
8. Han, B. et al. (2011) SHIFTX2: significantly improved protein chemical shift prediction. J. Biomol. NMR, 50, 43-57.
9. Johnson, B. A. and Blevins, R. A. (1994) NMR View: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR, 4, 603-614.
10. Lee, W. et al. (2012) PACSY, a relational database management system for protein structure and chemical shift analysis. J. Biomol. NMR, 54, 169-179.
11. Lee, W. et al. (2009) PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinformatics, 25, 2085-2087.
12. Lee, W. et al. (2014) PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J. Biomol. NMR., 60, 73-75.
13. McGuffin, L. J. et al. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
14. Murzin, A. G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
15. Shen, Y. et al. (2009) De novo protein structure generation from incomplete chemical shift assignments. J. Biomol. NMR, 43, 63-78.
16. Shen, Y. and Bax, A. (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J. Biomol. NMR, 56, 227-241.
17. Ulrich, E. L. et al. (2008) BioMagResBank. Nucleic Acids Res., 36, D402-D408.