Biology:CING (biomolecular NMR structure)
From HandWiki
A Janin Plot generated by CING from chain A, Arginine residue number 18 in the protein Dynein Light Chain, (PDB ID 1y4o). The blue region show likely angle combinations for helical residues, while the yellow areas display regions that are common to strand-like stretches. Some green background can be seen for residues that are in other types of regions. The image was taken from the residue page here at the NRG-CING [1] archive of validation reports
In biomolecular structure, CING stands for the Common Interface for NMR structure Generation and is known for structure and NMR data validation.[2]
NMR spectroscopy provides diverse data on the solution structure of biomolecules. CING combines many external programs and internalized algorithms to direct an author of a new structure or a biochemist interested in an existing structure to regions of the molecule that might be problematic in relation to the experimental data.
The source code is maintained open to the public at Google Code. There is a secure web interface iCing available for new data.
Applications
- 9000+ validation reports for existing Protein Data Bank structures in NRG-CING.[1]
- CING has been applied to automatic predictions in the CASD-NMR experiment with results available at CASD-NMR.
Validated NMR data
- Protein or Nucleic acid structure together called Biomolecular structure
- Chemical shift
- (Nuclear Overhauser effect) Distance restraint
- Dihedral angle restraint
- RDC or Residual dipolar coupling restraint
- NMR (cross-)peak
Software
Following software is used internally or externally by CING:
- 3DNA [3]
- Collaborative Computing Project for NMR
- CYANA (Software)
- DSSP (algorithm)
- MOLMOL [4]
- Matplotlib
- Nmrpipe
- PROCHECK/Aqua [5]
- POV-Ray
- ShiftX [6]
- TALOS+ [7]
- WHAT_CHECK [8]
- Wattos [9]
- XPLOR-NIH
- Yasara
Algorithms
Funding
The NRG-CING project was supported by the European Community grants 213010 (eNMR) and 261572 (WeNMR).
References
- ↑ 1.0 1.1 Doreleijers, J. F.; Vranken, W. F.; Schulte, C.; Markley, J. L.; Ulrich, E. L.; Vriend, G.; Vuister, G. W. (2011). "NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB". Nucleic Acids Research 40 (Database issue): D519–D524. doi:10.1093/nar/gkr1134. PMID 22139937.
- ↑ CING; an integrated residue-based structure validation program suite, Jurgen F. Doreleijers Alan W. Sousa da Silva, Elmar Krieger, Sander B. Nabuurs, Chris Spronk, Tim Stevens, Wim F. Vranken, Gert Vriend, Geerten W. Vuister (to be submitted).
- ↑ Lu and Olson. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature Protocols (2008) vol. 3 (7) pp. 1213-27
- ↑ Koradi et al. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph (1996) vol. 14 pp. 51-55
- ↑ Laskowski et al. AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J Biomol NMR (1996) vol. 8 (4) pp. 477-486
- ↑ Neal et al. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR (2003) vol. 26 (3) pp. 215-240
- ↑ Shen et al. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR (2009) vol. 44 (4) pp. 213-23
- ↑ Hooft et al. Errors in protein structures. Nature (1996) vol. 381 (6580) pp. 272-272
- ↑ Doreleijers, J. F.; Nederveen, A. J.; Vranken, W.; Lin, J.; Bonvin, A. M. J. J.; Kaptein, R.; Markley, J. L.; Ulrich, E. L. (2005). "BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures". Journal of Biomolecular NMR 32 (1): 1–12. doi:10.1007/s10858-005-2195-0. PMID 16041478.
- ↑ Kumar and Nussinov. Relationship between Ion Pair Geometries and Electrostatic Strengths in Proteins. Biophys.J. (2002) vol. 83 pp. 1595–1612
- ↑ Dombkowski and Crippen. Disulfide recognition in an optimized threading potential. Protein Engineering Design and Selection (2000) vol. 13 (10) pp. 679-689
- ↑ Ross. Peirce's criterion for the elimination of suspect experimental data. Journal of Engineering Technology (2003)
External links
- CING - includes tutorials and blog.
- iCing - web interface to CING.
- software - Google code with issue tracker and Wiki.
- NRG-CING - validation results on all PDB NMR structures.
- CASD-NMR CING - validation results of recent CASD-NMR predicted structures.
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