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The database contains also a smaller amount of NMR data from carbohydrates, cofactors and ligands. [1] These data are crossreferenced to 3D structures in the PDB when available. The NMR data are provided in the NMR-STAR file format and a number of format conversion tools are available at the site to convert files from NMR-STAR to other formats. [1]
The NMR sample is prepared in a thin-walled glass tube. Protein nuclear magnetic resonance is performed on aqueous samples of highly purified protein. Usually, the sample consists of between 300 and 600 microlitres with a protein concentration in the range 0.1 – 3 millimolar.
The Protein Data Bank was announced in October 1971 in Nature New Biology [10] as a joint venture between Cambridge Crystallographic Data Centre, UK and Brookhaven National Laboratory, US. Upon Hamilton's death in 1973, Tom Koetzle took over direction of the PDB for the subsequent 20 years.
database of intrinsic protein disorder annotation 3D structure protein databases, Protein sequence databases ModBase: Database of Comparative Protein Structure Models: Ursula Pieper, Ben Webb, Narayanan Eswar, Andrej Sali Roberto Sanchez UCSF, Sali Lab 3D structure protein databases PDBsum: Pictorial database of 3D structures in the Protein ...
A database that was developed and maintained by the publisher John Wiley & Sons. This database included more than 700,000 NMR, IR and MS Spectra, statistics specific to the NMR spectra are not listed. The NMR data includes 1 H, 13 C, 11 B, 15 N, 17 O, 19 F, 29 Si, and 31 P. The data were in the form of graphically displayed line lists.
Protein Data Bank in Europe (PDBe) Protein Data Bank Japan (PDBj) Biological Magnetic Resonance Data Bank (BMRB) Electron Microscopy Data Bank (EMDB). The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB. EMDB (UK) joined in 2021. Each member's site can accept structural data and ...
RefDB is a continuously updated resource that uses web-bots to query public databases (BMRB, GenBank, Protein Data Bank) and fetch assignment, sequence and structure data on a weekly basis. It then applies a series of data checking routines (using keywords to remove paramagnetic or denatured proteins) followed by a series of calculations to ...
Example of chemical shift index. The chemical shift index or CSI is a widely employed technique in protein nuclear magnetic resonance spectroscopy that can be used to display and identify the location (i.e. start and end) as well as the type of protein secondary structure (beta strands, helices and random coil regions) found in proteins using only backbone chemical shift data [1] [2] The ...
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