Oral Presentation 2014 International Biophysics Congress

The Protein Circular Dichroism Data Bank (PCDDB): A data sharing resource for structural biology (#112)

Robert W. Janes 1 , L. Whitmore 2 , B.A. Wallace 2
  1. School of Biological Sciences, Queen Mary University of London, London, UK
  2. Institute of Structural Biology, Birkbeck College, London, UK

            The Protein Circular Dichroism Data Bank (PCDDB) (http://pcddb.cryst.bbk.ac.uk) is a deposition database for protein circular dichroism (CD) spectroscopic data and metadata, with links to sequence and structure databases and citation references. It enables open access to raw, processed, and validated data associated with published studies, as well as providing depositors with a means of fulfilling granting body and journal data sharing requirements. The website also includes software for spectral analyses, and a link to a website for conversion to a wide variety of file formats, including the JCAMP-DX-CD format approved by IUPAC. Making these data available for meta-analyses opens the potential for their use in a wide range of applications, such as methodology development, comparisons of modelled and experimental structures, identification of new protein folds, and comparisons between wild type and mutant proteins.

            Since its original release of the 71 “gold standard” spectra that comprise the SP175 reference dataset that is widely used for CD analyses, the PCDDB holdings have grown to include both soluble and membrane proteins under different conditions, and thermal denaturation series; more than 500,000 files have been downloaded thus far by users across a wide range of disciplines. The data in the PCDDB have been used to create new bioinformatics tools and methodologies for analyses of circular dichroism spectra, in fulfilment of the original open data sharing aims.

(Supported by the U.K. Biotechnology and Biological Sciences Research Council, and the International Union of Pure and Applied Chemistry)