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- W2793670263 abstract "Circular Dichroism (CD) spectroscopy is widely used to determine the secondary structure content of proteins. However, more structural features than secondary structure alone contribute to the shape and magnitude of the spectra obtained by CD. The juxtapositioning of these secondary structure elements in its tertiary structure can also contribute to the CD spectrum of a protein for example. PDB2CD is an empirical-based approach to the prediction of CD spectra from protein atomic coordinates and here we present extensions to the original package1. The method combines three levels of structural features within the conformation of a protein; its percentage secondary structure content, the topological arrangement of discrete secondary structure elements, and the overall structural similarity of the query protein to the 71 proteins in the SP175 dataset, the ‘gold standard’ set obtained from the Protein Circular Dichroism Data Bank (PCDDB). The approach employed in PDB2CD was able to generate a significant number of the CD spectra associated with the 71 proteins in this dataset with excellent accuracy using a leave-one-out cross-validation process. The method also generated spectra in good agreement with those of a test set of 14 proteins from the PCDDB. PDB2CD is a user-friendly web-based package providing a novel approach to enable researchers to produce CD spectra from protein atomic coordinates. Our additions include, for example, an extended wavelength range for the predicted CD spectrum and the ability to download the image files. Available at: http://pdb2cd.cryst.bbk.ac.uk Support: BBSRC UK Grant (J019194) 1 Mavridis, L. and Janes, R.W. (2017) Bioinformatics 33: 56-63." @default.
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- W2793670263 date "2018-02-01" @default.
- W2793670263 modified "2023-09-30" @default.
- W2793670263 title "PDB2CD: A Web-Based Application for the Generation of Circular Dichroism Spectra from Protein Atomic Coordinates" @default.
- W2793670263 doi "https://doi.org/10.1016/j.bpj.2017.11.302" @default.
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