BioMagResBank
By E. Ulrich, H. Akutsu, J. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller and 6 more. Nucleic Acids Res., 2007
1,029 citations recorded by the source corpus.
The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pKa values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional 1H and 13C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/42648e8a0752407b8dd6bdb99910f500e701d15b
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In Materials Chemistry
- Ben M. Webb
- Santrupti Nerli
- Gaetano T. Montelione
- Nikolaos G. Sgourakis
- Yuanpeng Janet Huang
- Yang Zhang
- Andrej Sali
- Lena Buchner
In Molecular Biology
- Santrupti Nerli
- Nikolaos G. Sgourakis
- Gaetano T. Montelione
- Ben M. Webb
- Debora Marks
- Yuanpeng Janet Huang
- Yang Zhang
- Jinbo Xu
Citations in the corpus
- CS-ROSETTA (2018, methodology): “In addition, the toolbox consists of programs that allow rapid conversion of deposited NMR data in BMRB (Biological Magnetic Resonance Bank) (Ulrich et al., 2008) or NEF (NMR exchange format) (Gutmanas et al., 2015) file formats to Rosetta compatible file formats.”
- Distance Matrix-Based Approach to Protein Structure Prediction (2009, methodology): “The potentials for all the cross residue distances were then summed up and inserted into the energy function in CNS software.”
- Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, neutral): “BMRB hosts deposition sites in both the US (BMRB; www.bmrb.wisc.edu) and Japan (PDBj-BMRB; bmrbdep.pdbj.org) [ 18].”
- Combined automated NOE assignment and structure calculation with CYANA (2015, background): “…the chemical shift values for the same atom in different chemical shift lists are reported, as well as chemical shifts that deviate by more than 4 standard deviations from their average value in the BMRB chemical shift statistics (Ulrich et al. 2008), which is stored in the CYANA residue library.”
- Integrative structure modeling with the Integrative Modeling Platform (2017, background): “Publication of macromolecular structures includes deposition of coordinates and X-ray scattering factors, 67 NMR restraints, 90 and EM particle images.”
- Protein structure determination by combining sparse NMR data with evolutionary couplings (2015, positive): “The NMR resonance assignment table is prepared in either BMRB 2.x or 3.x format 38 .”