The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development. Issue 11 (15th June 2022)

• Record Type: Journal Article
• Authors: Ramalli, Sergio Gomes; Miles, Andrew John; Janes, Robert W.; Wallace, B.A.
• Is Part Of: Journal of molecular biology. Volume 434:Issue 11(2022)
• Publication Date: 2022-06-15
• Subjects: circular dichroism spectroscopy -- protein structural and spectroscopic database -- data deposition and accession -- protein stability and environmental effects -- resource for bioinformatics developments; CD circular dichroism -- IDP intrinsically disordered protein -- MRE mean residue ellipticity -- NMR nuclear magnetic resonance -- NRMSD normalised root mean square deviation -- PCDDB Protein Circular Dichroism Data Bank -- PCDDBid unique acquisition code for a PCDDB entry -- PDB Protein Data Bank -- SRCD synchrotron radiation circular dichroism -- HT high tension -- IntEnz enzyme classification; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2022.167441
• Languages: English
• ISSNs: 0022-2836

Abstract

Graphical abstract: Highlights: The PCDDB is a database for protein circular dichroism spectral data and metadata. Entries include cross-citations to sequence (UniProt) and structure (PDB) databases. Software for validation, comparisons, and identifying near-neighbours is included. It has been used for the development of new analysis methods. It is a resource for studies about protein structures and function. Abstract: The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk ] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB), AlphaFold, and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included. The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes.