NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

Autor: Doreleijers J.F., Vranken W.F., Schulte C., Markley J.L., Ulrich E.L., Vriend G., Vuister G.W.

Publikováno v: UnpayWall
ORCID
Microsoft Academic Graph
NARCIS
Europe PubMed Central
PubMed Central
DANS (Data Archiving and Networked Services)
ICT FP7 Publications Database
Nucleic Acids Research, 40, D519-524
Nucleic Acids Research

For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and preci

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::b4917fa78062a09fb8111199d2b2a9b4
https://academic.microsoft.com/#/detail/2619912946

BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

Autor: Doreleijers, J.F., Nederveen, A.J., Vranken, W., Lin, J., Bonvin, A.M.J.J., Kaptein, R., Markley, J.L., Ulrich, E.L., NMR-spectroscopie, NMR Spectroscopy 1, Dep Scheikunde

Publikováno v: Journal of Biomolecular NMR, 32, 1. Springer Netherlands
Journal of biomolecular NMR, 32(1), 1-12. Springer Netherlands

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 depo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e521df94b9da5db40e47a7e09d173b7c
https://doi.org/10.1007/s10858-005-2195-0

Biophysical and Solution Structure Analysis of Critical Residues Involved in the Interaction between the PupB N-Terminal Signaling Domain and PupR C-Terminal Cell Surface Signaling Domain from Pseudomonas capeferrum.

Autor: Sultana, Tajnin¹ (AUTHOR) tajnin.sultana@ndsu.edu, Morgan, David M.^1,2 (AUTHOR) dmmorgan@gmail.com, Jernberg, Beau D.^1,3 (AUTHOR) bjernberg18@gmail.com, Zak, Peyton¹ (AUTHOR) peytonzak6@gmail.com, Sinha, Sangita C.¹ (AUTHOR) sangita.sinha@ndsu.edu, Colbert, Christopher L.¹ (AUTHOR) sangita.sinha@ndsu.edu

Publikováno v: Biomolecules (2218-273X). Sep2024, Vol. 14 Issue 9, p1108. 15p.

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