scholarly journals DichroMatch at the protein circular dichroism data bank (DM@PCDDB): A web-based tool for identifying protein nearest neighbors using circular dichroism spectroscopy

2017 ◽  
Vol 27 (1) ◽  
pp. 10-13 ◽  
Author(s):  
Lee Whitmore ◽  
Lazaros Mavridis ◽  
B.A. Wallace ◽  
Robert W. Janes
Keyword(s):  
Circular Dichroism ◽  
Nearest Neighbors ◽  
Data Bank ◽  
Circular Dichroism Spectroscopy ◽  
Web Based ◽  
Circular Dichroism Data ◽  
Circular Dichroïsm

scholarly journals The Protein Circular Dichroism Data Bank, A Web-Based Site for Access to Circular Dichroism Spectroscopic Data

Structure ◽  
2010 ◽  
Vol 18 (10) ◽  
pp. 1267-1269 ◽  
Author(s):  
Lee Whitmore ◽  
Benjamin Woollett ◽  
Andrew J. Miles ◽  
Robert W. Janes ◽  
B.A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Spectroscopic Data ◽  
Data Bank ◽  
Web Based ◽  
Circular Dichroism Data ◽  
Circular Dichroïsm

Synchrotron radiation circular dichroism (SRCD) spectroscopy: an enhanced method for examining protein conformations and protein interactions

2010 ◽  
Vol 38 (4) ◽  
pp. 861-873 ◽  
Author(s):  
B.A. Wallace ◽  
Robert W. Janes
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Protein Interactions ◽  
Structural Information ◽  
Data Bank ◽  
Cd Spectroscopy ◽  
Circular Dichroism Spectroscopy ◽  
Protein Conformations ◽  
Mutant Proteins ◽  
Circular Dichroïsm

CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins, the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein–protein complex formation involving either induced-fit or rigid-body mechanisms, and protein–lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.

scholarly journals PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata

2010 ◽  
Vol 39 (suppl_1) ◽  
pp. D480-D486 ◽  
Author(s):  
Lee Whitmore ◽  
Benjamin Woollett ◽  
Andrew John Miles ◽  
D. P. Klose ◽  
Robert W. Janes ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Data Bank ◽  
Circular Dichroism Data ◽  
Circular Dichroïsm

scholarly journals The Protein Circular Dichroism Data Bank: A Resource for Data Sharing

2013 ◽  
Vol 104 (2) ◽  
pp. 567a
Author(s):  
Lee Whitmore ◽  
Benjamin Woollett ◽  
Robert W. Janes ◽  
B.A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Data Sharing ◽  
Data Bank ◽  
Circular Dichroism Data ◽  
Circular Dichroïsm

scholarly journals PCDDB: new developments at the Protein Circular Dichroism Data Bank

2016 ◽  
Vol 45 (D1) ◽  
pp. D303-D307 ◽  
Author(s):  
Lee Whitmore ◽  
Andrew John Miles ◽  
Lazaros Mavridis ◽  
Robert W. Janes ◽  
B.A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Data Bank ◽  
New Developments ◽  
Circular Dichroism Data ◽  
Circular Dichroïsm

Wavelength Calibration Uncertainty in Protein Circular Dichroism Data Bank Spectra

2021 ◽  
pp. 000370282199074
Author(s):  
Christopher Jones
Keyword(s):  
Circular Dichroism ◽  
Statistical Evaluation ◽  
Data Bank ◽  
Peak Height ◽  
Order Structure ◽  
Wavelength Calibration ◽  
Calibration Uncertainty ◽  
The Difference ◽  
Circular Dichroism Data ◽  
Circular Dichroïsm

Algorithms to objectively compare the circular dichroism spectra of biopharmaceuticals, as a measure of consistent higher order structure, are sensitive to errors in spectropolarimeter wavelength calibration. A public database, the Protein Circular Dichroism Data Bank contains 108 unique calibration spectra of d-camphor-10-sulphonic acid, mainly collected on synchrotron-based instruments. Deconvolution of these spectra and statistical evaluation of the peaks located near 290 and 190 nm shows significant mean peak wavelength differences between instruments, with data ranges of 1.8 and 2.3 nm. Peak positions and peak height ratios for individual instruments changed significantly through time, and the difference between wavelength maxima was instrument dependent.

scholarly journals Protein circular dichroism data bank (PCDDB): Data bank and website design

Chirality ◽  
2006 ◽  
Vol 18 (6) ◽  
pp. 426-429 ◽  
Author(s):  
Lee Whitmore ◽  
Robert W. Janes ◽  
B. A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Data Bank ◽  
Website Design ◽  
Circular Dichroism Data ◽  
Circular Dichroïsm
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