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BioMagResBank
2007
Nucleic Acids Research
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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. ...
BioMagResBank (4, 5) (BMRB, www.bmrb.wisc.edu) is designed to empower structural biologists, macromolecular chemists and other scientists who use these data to address questions concerning a variety ...
doi:10.1093/nar/gkm957
pmid:17984079
pmcid:PMC2238925
fatcat:t5ldblf4cjbs7ojw5y4xriuoym
PDBj-BMRB : Publishing NMR Spectroscopy Derived Data of BioMagResBank in Structured Data Formats, XML and RDF(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)
2013
Seibutsu Butsuri
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The PDBj-BMRB (bmrbdep.protein.osaka-u.ac.jp) at Osaka University operates a BioMagResBank (BMRB) site, which accepts data depositions and carries out data processing and annotation in close collaboration ...
doi:10.2142/biophys.53.s286_3
fatcat:gs5cgv4akrfxriqsubclnvz6hy
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
2005
Proteins: Structure, Function, and Bioinformatics
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Curated restraints were obtained from the BioMagResBank FRED database. ...
We used restraints in NMR-STAR 3 format from the BioMagResBank 19 Filtered Restraints Database (FRED), corresponding to a set of 545 entries with distance restraints originally deposited in XPLOR/CNS, ...
This problem was recently solved for 545 proteins, for which curated restraints are now available from the BioMagResBank (BMRB). 19 This database is described in detail in another article. 20 As described ...
doi:10.1002/prot.20408
pmid:15822098
fatcat:22ty2pawnzfv5esyljaeumdbfe
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions
2008
Journal of Biomolecular NMR
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We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. ...
Abstract We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. ...
The BioMagResBank (BMRB, http://www. bmrb.wisc.edu/), the repository for experimental and derived data gathered from NMR spectroscopic studies of biological molecules , has been a member of the Worldwide ...
doi:10.1007/s10858-008-9221-y
pmid:18288446
pmcid:PMC2268728
fatcat:tbfte43uefc4pohe6fncp5xy2y
An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database
2012
Journal of Biomolecular NMR
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demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank ...
These results suggest that the NMR data deposited by RSGI have contributed to the quality improvement of BioMagResBank. ...
For the purpose of collecting and archiving NMR experimental data, the BioMagResBank (BMRB) was established as the standard public database for NMR data of biomolecules (Seavey et al. 1991; Ulrich et ...
doi:10.1007/s10858-012-9641-6
pmid:22689068
pmcid:PMC4308039
fatcat:a3kf7viodnck3jdtieliaoqmgm
PyBMRB: Data visualization tool for BioMagResBank
2021
Proceedings of the 20th Python in Science Conference
unpublished
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The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB https://bmrb.io), founded in 1988, is the international, open archive for data generated by Nuclear Magnetic Resonance (NMR) spectroscopy ...
The BioMagResBank (BMRB) [UAD + 07] provides high-quality, curated NMR spectroscopic data collected from biologically important molecules such as proteins, nucleic acids, carbohydrates, and metabolites ...
doi:10.25080/majora-1b6fd038-00a
fatcat:42j52hi66ren5gjouae3hjhowe
ARIA: automated NOE assignment and NMR structure calculation
2003
Bioinformatics
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al., ARIA
BioMagResBank
NMR Experiment
NOE Spectrum
Iterative NOE assigment
and structure calculation
Submission
Processing ...
Therefore, we integrated a Python module (written by Jurgen Doreleijers, BMRB) that enables us to write BioMagResBank compliant STAR files. ...
doi:10.1093/bioinformatics/19.2.315
pmid:12538267
fatcat:eggjvsztfzg3hbjcadih4sg4pm
1H, 13C, and 15N chemical shift assignments for the N-terminal extracellular domain of T-cadherin
2006
Journal of Biomolecular NMR
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Chemical shift values for human T-cadherin (1-105) have been deposited in the BioMagResBank under accession number 7268. ...
Chemical shift values for human T-cadherin (1-105) have been deposited in the BioMagResBank under accession number 7268. ...
doi:10.1007/s10858-006-9106-x
pmid:17180550
fatcat:4xy7x5wdanbcbo7i2x5hmvqv54
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
2016
Journal of Biomedical Semantics
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The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. ...
Findings
Background The BioMagResBank (BMRB; http://www.bmrb.wisc.edu/) is a worldwide data repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies ...
(PDF 6814 kb) Abbreviations BMRB: BioMagResBank; MECP2: methyl-CpG-binding protein 2; NMR: nuclear magnetic resonance; OMIM: Online Mendelian Inheritance in Man; OWL: web ontology language; RDF: resource ...
doi:10.1186/s13326-016-0057-1
pmid:27927232
pmcid:PMC5143449
fatcat:kidpbvthwbgzjko7jvgesbepqm
Prototype Access To Selected Datasets
2017
Zenodo
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NMR Data at BioMagResBank (BMRB) -Not yet integrated to dataset prototype. ...
NMR Data at BioMagResBank (BMRB) -a European mirror maintained by project partner CIRMPP. It offers RESTful API to obtain NMR data related to BMRB entry. Other API offers HTML output. 4. ...
doi:10.5281/zenodo.1002680
fatcat:fljocvyfcffejo75zn7jlypm5u
Coexisting order and disorder within a common 40-residue amyloid-β fibril structure in Alzheimer's disease brain tissue
2018
Chemical Communications
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(B) Site-specific differences in 13 C chemical shifts between brainderived A40 fibrils from patient 1 of Lu et al. 6 (BioMagResBank code 19009) and brainderived A40 fibrils discussed in this paper. ...
Figure S4 : (A) Site-specific differences in 13 C chemical shifts between A40 fibrils prepared in vitro by Paravastu et al. 1 (BioMagResBank code 18129) and brain-derived A40 fibrils discussed in this ...
doi:10.1039/c8cc01967c
pmid:29707712
fatcat:wzdchc3hlrey7duurys425mota
Statistical evaluation of NMR backbone resonance assignment
2006
International Journal of Bioinformatics Research and Applications
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The protein datasets used in the experiment were simulated from known protein entries in BioMagResBank. ...
The values we chose for the standard deviations (see Section 3 for detailed values) are based on the statistical results in BioMagResBank (http://www.bmrb.wisc.edu). ...
doi:10.1504/ijbra.2006.009765
pmid:18048159
fatcat:pxuyri723zgircg2wqm4gfzbge
Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules
1998
Acta Crystallographica Section D: Biological Crystallography
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They also include HyperText links to the SwissProt protein sequences database (Bairoch & Boeckmann, 1994) BioMagResBank (BMRB) NMR structural database (Seavey et al., 1991) , the Enzyme Commission Database ...
esther (http://www.ensam.inra.fr/cholinesterase/) or Archive of Obsolete PDB Entries databases (http://pdbobs.sdsc.edu/PDBObs.cgi) and those that provide additional experimental information such as the BioMagResBank ...
doi:10.1107/s0907444998009378
pmid:10089483
fatcat:v5y22reejbasjestysnipsi4yu
Annotation and Curation of the Protein Data Bank
2009
Nature Precedings
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***BMRB, BioMagResBank, University of Wisconsin, Wisconsin, USA. wwPDB: Recent Projects www.wwpdb.org/docs.html 2008 Advisory Committee www.wwpdb.org
Nature Precedings : doi:10.1038/npre.2009.3379.1 ...
logistics among wwPDB partners. wwPDB
• Formalization of current working practice
• Members
-RCSB PDB (Research Collaboratory for
Structural Bioinformatics)
-PDBj (Osaka University)
-PDBe (EMBL-EBI)
-BioMagResBank ...
doi:10.1038/npre.2009.3379.1
fatcat:w5tg7kmykvcknalmldp7gippny
1H, 13C, and 15N NMR assignments of the Pyrococcus abyssi DNA polymerase II intein
2011
Biomolecular NMR Assignments
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One of the K69 H ε has a chemical shift of 1.11 ppm and put it as the lowest chemical shift of lysine H ε protons reported in the BioMagResBank (http://www.bmrb.wisc.edu). ...
The chemical shifts have been deposited in the BioMagResBank under accession number 17418. Figure 1 . 1 1 H-15 N HSQC spectrum of the Pab PolII intein backbone assignments. ...
doi:10.1007/s12104-011-9307-4
pmid:21519863
pmcid:PMC3166996
fatcat:d2sn2xwapfekzncqmvagm5z2ei
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