Related ArticlesBioMagResBank 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 restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA.
[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 database with sets of experimental NMR constraints corresponding to the
BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank.
Related Articles BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank.
J Biomol NMR. 2003 Jun;26(2):139-46
Authors: Doreleijers JF, Mading S, Maziuk D, Sojourner K, Yin L, Zhu J, Markley JL, Ulrich EL
Experimental constraints associated with NMR structures are available from the...
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[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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Improved Resolution in Dipolar NMR Spectra Using Constant Time Evolution PISEMA Exper
Improved Resolution in Dipolar NMR Spectra Using Constant Time Evolution PISEMA Experiment.
Related Articles Improved Resolution in Dipolar NMR Spectra Using Constant Time Evolution PISEMA Experiment.
Chem Phys Lett. 2010 Jul 9;494(1-3):104-110
Authors: Gopinath T, Veglia G
The atomic structure of small molecules and polypeptides can be attained from anisotropic NMR parameters such as dipolar couplings (DC) and chemical shifts (CS). Separated local field experiments resolve DC and CS correlations into two dimensions. However, crowded NMR...
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 databases DOCR and FRED containing converted and filtered sets of exper
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