Related ArticlesBioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank.
Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of "Magnetic Resonance" (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data type using a semi-automated protocol. A new software program called Wattos was then used to parse and archive the data in a relational database. From the total number of MR file blocks annotated as constraints, it proved possible to parse 84% (3337/3975). The constraint lists that were parsed correspond to three data types (2511 distance, 788 dihedral angle, and 38 residual dipolar couplings lists) from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists), and DYANA/DIANA (405 lists). These constraints were then mapped to a developmental version of the BioMagResBank (BMRB) data model. A total of 31 data types originating from 16 programs have been classified, with the NOE distance constraint being the most commonly observed. The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu).
[Question from NMRWiki Q&A forum] transfer of data sets/pulse sequences from Xwinnmr/DRX to Avance III/topspin
transfer of data sets/pulse sequences from Xwinnmr/DRX to Avance III/topspin
How do I transfer data sets ( with pulse sequences for measurements of various cross- -relaxtion rates) collected under Xwinnmr DRX console to an Avance III console with topspin 3. (on the same instrument/probe). Is it a straigtforward copying of the data folders, or are there any caveats involved? thank you for any input
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[NMR paper] BioMagResBank databases DOCR and FRED containing converted and filtered sets of exper
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures.
Related Articles BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures.
J Biomol NMR. 2005 May;32(1):1-12
Authors: Doreleijers JF, Nederveen AJ, Vranken W, Lin J, Bonvin AM, Kaptein R, Markley JL, Ulrich EL
We present two new databases of NMR-derived distance and dihedral angle...
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11-25-2010 08:21 PM
[NMR paper] Automated analysis of large sets of heteronuclear correlation spectra in NMR-based dr
Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery.
Related Articles Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery.
J Med Chem. 2002 Dec 19;45(26):5649-54
Authors: Damberg CS, Orekhov VY, Billeter M
Drug discovery procedures based on NMR typically require the analysis of thousands of NMR spectra. For example, in "SAR by NMR", two-dimensional NMR spectra are recorded for a target protein mixed with ligand candidates from a comprehensive library of...
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NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental
NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.
Related Articles NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.
Nucleic Acids Res. 2010 Jul 1;38 Suppl:W628-32
Authors: Heller DM, Giorgetti A
Nuclear magnetic resonance (NMR) spectroscopy together with X-ray crystallography, are the main techniques used for the determination of high-resolution 3D structures of biological molecules. The output of an NMR experiment includes a set of lower and upper...
Composite Alignment Media for the Measurement of Independent Sets of NMR Residual Dipolar Couplings
Composite Alignment Media for the Measurement of Independent Sets of NMR Residual Dipolar Couplings
Ke Ruan and Joel R. Tolman
J. Am. Chem. Soc.; 2005; 127(43) pp 15032 - 15033;
Abstract:
The measurement of independent sets of NMR residual dipolar couplings (RDCs) in multiple alignment media can provide a detailed view of biomolecular structure and dynamics, yet remains experimentally challenging. It is demonstrated here that independent sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a...
BioMagResBank database with sets of experimental NMR constraints corresponding to the
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