Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

Autor: Yokochi, M. Kobayashi, N. Ulrich, E.L. Kinjo, A.R. Iwata, T. Ioannidis, Y.E. Livny, M. Markley, J.L. Nakamura, H. Kojima, C. Fujiwara, T.

Background: 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. The NMR data archived in NMR-STAR ASCII fo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od______2127::28bb428fdbaccdd2502816aa981ffb60
https://pergamos.lib.uoa.gr/uoa/dl/object/uoadl:3070988

Outcome of the First wwPDB Hybrid / Integrative Methods Task Force Workshop

Autor: Sali, A., Berman, H.M., Schwede, T., Trewhella, J., Kleywegt, G., Burley, S.K., Markley, J., Nakamura, H., Adams, P., Bonvin, A.M.J.J., Wah, C., Dal Peraro, M., Di Maio, F., Ferrin, T.E., Grünewald, K., Gutmanas, A., Henderson, R., Hummer, G., Iawsaki, K., Johnson, G., Lawson, C.L., Meiler, J., Marti-Renom, M.A., Montelione, G.T., Nilges, M., Nussinov, R., Patwardhan, A., Rappsilber, J., Read, R.J., Saibil, Helen R., Schröder, G.F., Schwieters, C., Seidel, C.A.M., Svergun, D., Topf, Maya, Ulrich, E.L., Velankar, S., Westbrook, J.D.

Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrativ

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=core_ac_uk__::e5c019dc3bb5464c457b3873c0a94391
https://eprints.bbk.ac.uk/id/eprint/12322/1/Sali_et_al_Structure_2015.pdf

BioMagResBank

Autor: Ulrich, E.L., Akutsu, H., Doreleijers, J., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C.F., Tolmie, D.E., Wenger, R.K., Yao, H., Markley, J.L.

Publikováno v: Nucleic Acids Research, 36, D402-8
Nucleic Acids Research
Nucleic Acids Research, 36, Database issue, pp. D402-8

Contains fulltext : 70130.pdf (Publisher’s version ) (Open Access) 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 mole

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a4653b9a2255a49811f6a594f6aaddfc
http://hdl.handle.net/2066/70130

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

Autor: Nederveen, A.J., Doreleijers, J.F., Vranken, W., Miller, Z., Spronk, C.A.E.M., Nabuurs, S.B., Guntert, P., Livny, M., Markley, J.L., Nilges, M., Ulrich, E.L., Kaptein, R., Bonvin, A.M.J.J., NMR-spectroscopie, NMR Spectroscopy 1, Dep Scheikunde

Publikováno v: Proteins, 59(4), 662-672. Wiley-Liss Inc.
Proteins: Structure function and bioinformatics, 59, 662. Wiley-Liss Inc.
Proteins-Structure Function and Bioinformatics, 59, 662-72
Proteins-Structure Function and Bioinformatics, 59, 4, pp. 662-72

State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500 proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints we

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cecc7c1c7463376fde519fe4634dea88
https://pubmed.ncbi.nlm.nih.gov/15822098

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