PDB2CD

Quick Instructions

General Advice

PDB2CD is a web server for the calculation of Circular Dichroism spectra of a protein, given their crystallographic data file. The web server uses the structure of a protein to predict it's CD spectrum. In order to do so it amalgamates structural features from secondary structure content, more sophisticated topological features and protein structure fold recognition techniques (CE).

Server Input

- Upload PDB: If you have your own pdb file, click on browse and upload your file to the server.

- Give a PDB Code: Provide the 4 digits pdb code of the protein you want to predict.


Result Page

The result page is split into four panes:

- Top Left: The visual representation of the predicted spectrum, and a link to a file with a two column format.

- Top Right: (Optional) If the user has checked against a pdb code, the server will download the image of the protein from RCSB, which is shown. In case the user uploads his own file, instead of the protein visualization the bottom right pane is shown in this position.

- Bottom Left: The topology of the pdb structure is shown, all the secondary element connections grouped according to three types alpha to alpha, alpha to beta and beta to beta.

- Bottom Right: The secondary structure map of the SP175 data set is shown as blue dots on the scatter plot and the input protein as a red star.

Banner Image

Cite

If you use PDB2CD, please quote

In using PDB2CD please cite: Mavridis, L,. and Janes, R.W.. (2017) PDB2CD : A web-based application for the generation of circular dichroism spectra from protein atomic coordinates. Bioinformatics 33: 56-63.

Contact

Dr. Robert W. Janes - r.w.janes at qmul.ac.uk

Elliot D. Drew - e.drew at qmul.ac.uk

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