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BioMagResBank

E. L. Ulrich, H. Akutsu, J. F. Doreleijers, Y. Harano, Y. E. Ioannidis, J. Lin, M. Livny, S. Mading, D. Maziuk, Z. Miller, E. Nakatani, C. F. Schulte (+4 others)
2007 Nucleic Acids Research  
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)

Masashi Yokochi
2013 Seibutsu Butsuri  
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

Aart J. Nederveen, Jurgen F. Doreleijers, Wim Vranken, Zachary Miller, Chris A.E.M. Spronk, Sander B. Nabuurs, Peter Güntert, Miron Livny, John L. Markley, Michael Nilges, Eldon L. Ulrich, Robert Kaptein (+1 others)
2005 Proteins: Structure, Function, and Bioinformatics  
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

John L. Markley, Eldon L. Ulrich, Helen M. Berman, Kim Henrick, Haruki Nakamura, Hideo Akutsu
2008 Journal of Biomolecular NMR  
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

Naohiro Kobayashi, Yoko Harano, Naoya Tochio, Eiichi Nakatani, Takanori Kigawa, Shigeyuki Yokoyama, Steve Mading, Eldon L. Ulrich, John L. Markley, Hideo Akutsu, Toshimichi Fujiwara
2012 Journal of Biomolecular NMR  
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

Kumaran Baskaran, Jonathan Wedell, Eldon Ulrich, Jeffery Hoch, John Markley
2021 Proceedings of the 20th Python in Science Conference   unpublished
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

J. P. Linge, M. Habeck, W. Rieping, M. Nilges
2003 Bioinformatics  
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

Eunjung Bang, Daniel Häussinger, Jörg Stetefeld, Thomas Ahrens, Stephan Grzesiek, Sonja A. Dames
2006 Journal of Biomolecular NMR  
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

Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
2016 Journal of Biomedical Semantics  
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

Kulhanek
2017 Zenodo  
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

Ujjayini Ghosh, Wai-Ming Yau, Robert Tycko
2018 Chemical Communications  
(B) Site-specific differences in 13 C chemical shifts between brainderived A40 fibrils from patient 1 of Lu et al. 6 (BioMagResBank code 19009) and brainderived A40 fibrils discussed in this paper.  ...  Figure S4 : (A) Site-specific differences in 13 C chemical shifts between A40 fibrils prepared in vitro by Paravastu et al. 1 (BioMagResBank code 18129) and brain-derived A40 fibrils discussed in this  ... 
doi:10.1039/c8cc01967c pmid:29707712 fatcat:wzdchc3hlrey7duurys425mota

Statistical evaluation of NMR backbone resonance assignment

Guohui Lin, Xiang Wan, Theodore Tegos, Yingshu Li
2006 International Journal of Bioinformatics Research and Applications  
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

Joel L. Sussman, Dawei Lin, Jiansheng Jiang, Nancy O. Manning, Jaime Prilusky, Otto Ritter, Enrique E. Abola
1998 Acta Crystallographica Section D: Biological Crystallography  
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

Jasmine Young, RCSB PDBj PDBe Protein Data Bank
2009 Nature Precedings  
***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

Jiajing Liu, Zhenming Du, Clayton D. Albracht, Roshni O. Naidu, Kenneth V. Mills, Chunyu Wang
2011 Biomolecular NMR Assignments  
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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